Exception in thread "main" java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
	at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
	at java.awt.Window.<init>(Window.java:536)
	at java.awt.Frame.<init>(Frame.java:420)
	at java.awt.Frame.<init>(Frame.java:385)
	at javax.swing.JFrame.<init>(JFrame.java:189)
	at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338)

 *** Bismark methylation extractor version v0.22.3 ***

Trying to determine the type of mapping from the SAM header line of file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam
Treating file(s) as paired-end data (as extracted from @PG line)

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

Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28)

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark paired-end SAM format specified (default)
Number of cores to be used: 28
Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/gscratch/scrubbed/sr320/071521-cvBS')


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:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>12M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >12M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 12M_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/12M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/12M_R2_val_2.fq.gz"

Now reading in Bismark result file 12M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Processed lines: 97000000
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Processed lines: 100500000
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Processed lines: 95000000
Processed lines: 98500000
Processed lines: 100000000
Processed lines: 100500000
Processed lines: 97000000
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Processed lines: 100000000
Processed lines: 96000000
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Processed lines: 100500000
Processed lines: 97500000
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Processed lines: 99000000
Processed lines: 98500000
Processed lines: 98000000
Processed lines: 97000000
Processed lines: 96000000
Processed lines: 101000000
Processed lines: 100500000
Now waiting for all child processes to complete
Processed lines: 99000000
Processed lines: 95500000
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Processed lines: 97500000
Processed lines: 95000000
Processed lines: 100000000
Finished processing child process. Exiting..
Processed lines: 97500000
Processed lines: 100500000
Processed lines: 96500000
Processed lines: 96000000
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Processed lines: 95500000
Processed lines: 100000000
Processed lines: 99500000
Processed lines: 95500000
Processed lines: 97000000
Processed lines: 99000000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 97500000
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Processed lines: 101000000
Processed lines: 99500000
Processed lines: 96000000
Processed lines: 101000000
Processed lines: 98000000
Processed lines: 100500000
Processed lines: 95500000
Finished processing child process. Exiting..
Processed lines: 101000000
Processed lines: 98000000
Finished processing child process. Exiting..
Processed lines: 96500000
Processed lines: 97000000
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Processed lines: 96000000
Processed lines: 95500000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 99500000
Processed lines: 96000000
Processed lines: 100500000
Processed lines: 100000000
Processed lines: 97500000
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Processed lines: 100000000
Processed lines: 97000000
Processed lines: 96500000
Processed lines: 98500000
Processed lines: 101000000
Processed lines: 96000000
Processed lines: 98500000
Processed lines: 97000000
Finished processing child process. Exiting..
Processed lines: 97500000
Processed lines: 98000000
Processed lines: 96500000
Processed lines: 96000000
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Processed lines: 100000000
Processed lines: 96500000
Processed lines: 101000000
Processed lines: 100500000
Processed lines: 98000000
Processed lines: 100000000
Processed lines: 99500000
Processed lines: 96500000
Processed lines: 98500000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 97500000
Processed lines: 97000000
Processed lines: 99000000
Processed lines: 96500000
Processed lines: 99000000
Processed lines: 97500000
Processed lines: 98500000
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Processed lines: 97000000
Processed lines: 99500000
Processed lines: 100500000
Processed lines: 96500000
Processed lines: 97000000
Processed lines: 101000000
Processed lines: 98500000
Processed lines: 100500000
Processed lines: 100000000
Processed lines: 97000000
Processed lines: 99000000
Processed lines: 101000000
Finished processing child process. Exiting..
Processed lines: 98000000
Processed lines: 97500000
Processed lines: 99500000
Finished processing child process. Exiting..
Processed lines: 97000000
Processed lines: 99500000
Processed lines: 98000000
Processed lines: 98500000
Processed lines: 99000000
Processed lines: 97500000
Processed lines: 100000000
Processed lines: 101000000
Processed lines: 97000000
Processed lines: 97500000
Processed lines: 99000000
Processed lines: 101000000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 97500000
Processed lines: 99500000
Processed lines: 98500000
Finished processing child process. Exiting..
Processed lines: 98000000
Processed lines: 100000000
Processed lines: 97500000
Processed lines: 100000000
Processed lines: 98500000
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Processed lines: 99500000
Processed lines: 100500000
Processed lines: 98000000
Processed lines: 97500000
Processed lines: 98000000
Processed lines: 99500000
Processed lines: 101000000
Processed lines: 98000000
Processed lines: 100000000
Processed lines: 99000000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 98000000
Processed lines: 100500000
Processed lines: 99000000
Processed lines: 99500000
Processed lines: 100000000
Processed lines: 101000000
Processed lines: 98500000
Processed lines: 98000000
Processed lines: 98500000
Processed lines: 100000000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 100500000
Processed lines: 99500000
Processed lines: 101000000
Processed lines: 99000000
Processed lines: 98500000
Processed lines: 101000000
Finished processing child process. Exiting..
Processed lines: 99500000
Processed lines: 100000000
Processed lines: 100500000
Processed lines: 99000000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 99000000
Processed lines: 100500000
Processed lines: 99000000
Processed lines: 101000000
Processed lines: 100000000
Processed lines: 99500000
Finished processing child process. Exiting..
Processed lines: 99000000
Processed lines: 100500000
Processed lines: 101000000
Processed lines: 100000000
Processed lines: 99500000
Processed lines: 99000000
Processed lines: 101000000
Finished processing child process. Exiting..
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 100000000
Processed lines: 99500000
Processed lines: 101000000
Processed lines: 100500000
Processed lines: 100000000
Finished processing child process. Exiting..
Processed lines: 99500000
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 101000000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 100000000
Processed lines: 101000000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 100500000
Processed lines: 100000000
Processed lines: 100500000
Processed lines: 101000000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 101000000
Processed lines: 100500000
Processed lines: 101000000
Processed lines: 101000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 101000000
Finished processing child process. Exiting..
Processed lines: 101000000
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 101143882 lines in total
Total number of methylation call strings processed: 202287764

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2725400659

Total methylated C's in CpG context:	47153262
Total methylated C's in CHG context:	1834477
Total methylated C's in CHH context:	7382974

Total C to T conversions in CpG context:	302909324
Total C to T conversions in CHG context:	481680820
Total C to T conversions in CHH context:	1884439802

C methylated in CpG context:	13.5%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		12M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 12M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 12M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_12M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>13M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >13M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 13M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 13M_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/13M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/13M_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 109000000
Finished processing child process. Exiting..
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Processed lines: 107000000
Processed lines: 112500000
Finished processing child process. Exiting..
Processed lines: 106500000
Processed lines: 110000000
Processed lines: 106500000
Processed lines: 107500000
Processed lines: 112500000
Processed lines: 105500000
Processed lines: 111500000
Processed lines: 112000000
Processed lines: 109000000
Processed lines: 108000000
Processed lines: 109500000
Processed lines: 111000000
Processed lines: 108500000
Processed lines: 110000000
Processed lines: 111500000
Finished processing child process. Exiting..
Processed lines: 106500000
Processed lines: 112500000
Processed lines: 109000000
Processed lines: 107000000
Processed lines: 107500000
Processed lines: 111000000
Finished processing child process. Exiting..
Processed lines: 108500000
Processed lines: 107500000
Processed lines: 107000000
Processed lines: 107000000
Processed lines: 110500000
Processed lines: 108000000
Processed lines: 107000000
Processed lines: 112000000
Finished processing child process. Exiting..
Processed lines: 112500000
Processed lines: 109500000
Processed lines: 106000000
Processed lines: 108500000
Processed lines: 110000000
Processed lines: 111500000
Processed lines: 109000000
Processed lines: 110500000
Processed lines: 112000000
Processed lines: 107000000
Processed lines: 109500000
Processed lines: 111500000
Processed lines: 107500000
Processed lines: 108000000
Processed lines: 109000000
Processed lines: 107500000
Processed lines: 108000000
Finished processing child process. Exiting..
Processed lines: 111000000
Processed lines: 107500000
Processed lines: 108500000
Processed lines: 107500000
Processed lines: 112500000
Processed lines: 110000000
Processed lines: 109000000
Processed lines: 106500000
Processed lines: 110500000
Processed lines: 112000000
Processed lines: 109500000
Processed lines: 111000000
Processed lines: 112500000
Processed lines: 110000000
Processed lines: 107500000
Processed lines: 112000000
Processed lines: 108000000
Processed lines: 108500000
Finished processing child process. Exiting..
Processed lines: 109500000
Processed lines: 108000000
Processed lines: 108500000
Processed lines: 111500000
Processed lines: 108000000
Processed lines: 109000000
Processed lines: 108000000
Finished processing child process. Exiting..
Processed lines: 110500000
Processed lines: 109500000
Processed lines: 107000000
Processed lines: 112500000
Processed lines: 111000000
Processed lines: 110000000
Processed lines: 111500000
Processed lines: 110500000
Processed lines: 108000000
Processed lines: 112500000
Processed lines: 108500000
Processed lines: 109000000
Processed lines: 110000000
Processed lines: 108500000
Processed lines: 109000000
Processed lines: 112000000
Finished processing child process. Exiting..
Processed lines: 108500000
Processed lines: 109500000
Processed lines: 108500000
Processed lines: 111000000
Processed lines: 110000000
Processed lines: 107500000
Processed lines: 111500000
Finished processing child process. Exiting..
Processed lines: 112000000
Processed lines: 110500000
Processed lines: 111000000
Processed lines: 108500000
Processed lines: 109500000
Processed lines: 110500000
Processed lines: 109000000
Processed lines: 109000000
Processed lines: 109500000
Processed lines: 112500000
Processed lines: 110000000
Processed lines: 109000000
Processed lines: 109000000
Processed lines: 111500000
Processed lines: 110500000
Processed lines: 112000000
Processed lines: 108000000
Processed lines: 112500000
Processed lines: 111000000
Processed lines: 111500000
Finished processing child process. Exiting..
Processed lines: 109000000
Processed lines: 111000000
Processed lines: 110000000
Processed lines: 109500000
Processed lines: 109500000
Processed lines: 110000000
Processed lines: 110500000
Processed lines: 109500000
Finished processing child process. Exiting..
Processed lines: 109500000
Processed lines: 112000000
Processed lines: 111000000
Processed lines: 112500000
Processed lines: 108500000
Processed lines: 111500000
Processed lines: 112000000
Processed lines: 109500000
Processed lines: 111500000
Processed lines: 110500000
Processed lines: 110000000
Processed lines: 110000000
Processed lines: 110500000
Finished processing child process. Exiting..
Processed lines: 111000000
Processed lines: 110000000
Processed lines: 110000000
Processed lines: 112500000
Processed lines: 111500000
Processed lines: 112000000
Processed lines: 109000000
Processed lines: 112500000
Processed lines: 110000000
Processed lines: 112000000
Processed lines: 111000000
Processed lines: 110500000
Finished processing child process. Exiting..
Processed lines: 110500000
Processed lines: 111000000
Processed lines: 111500000
Processed lines: 110500000
Processed lines: 110500000
Finished processing child process. Exiting..
Processed lines: 112000000
Processed lines: 112500000
Processed lines: 109500000
Processed lines: 110500000
Processed lines: 112500000
Processed lines: 111500000
Processed lines: 111000000
Processed lines: 111000000
Processed lines: 111500000
Processed lines: 112000000
Processed lines: 111000000
Processed lines: 111000000
Finished processing child process. Exiting..
Processed lines: 112500000
Finished processing child process. Exiting..
Processed lines: 110000000
Processed lines: 111000000
Processed lines: 111500000
Processed lines: 112000000
Processed lines: 112000000
Processed lines: 111500000
Finished processing child process. Exiting..
Processed lines: 112500000
Processed lines: 111500000
Processed lines: 111500000
Processed lines: 110500000
Processed lines: 111500000
Finished processing child process. Exiting..
Processed lines: 112000000
Processed lines: 112500000
Processed lines: 112500000
Processed lines: 112000000
Processed lines: 112000000
Processed lines: 112000000
Processed lines: 111000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 112000000
Processed lines: 112500000
Processed lines: 112500000
Processed lines: 112500000
Processed lines: 112500000
Finished processing child process. Exiting..
Processed lines: 111500000
Processed lines: 112500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 112000000
Processed lines: 112500000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 112840017 lines in total
Total number of methylation call strings processed: 225680034

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2895601370

Total methylated C's in CpG context:	49622161
Total methylated C's in CHG context:	2041725
Total methylated C's in CHH context:	8365379

Total C to T conversions in CpG context:	336438857
Total C to T conversions in CHG context:	523821535
Total C to T conversions in CHH context:	1975311713

C methylated in CpG context:	12.9%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		13M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 13M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 13M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_13M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>16F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >16F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 16F_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 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 16F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/16F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/16F_R2_val_2.fq.gz"
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Processed lines: 89500000
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Processed lines: 92500000
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Processed lines: 86500000
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Processed lines: 90000000
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Processed lines: 86500000
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Processed lines: 91000000
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Processed lines: 88000000
Processed lines: 93500000
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Processed lines: 94000000
Processed lines: 91000000
Processed lines: 86500000
Processed lines: 87000000
Processed lines: 89500000
Processed lines: 93000000
Processed lines: 92500000
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Processed lines: 87500000
Processed lines: 90000000
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Finished processing child process. Exiting..
Processed lines: 87500000
Processed lines: 90500000
Processed lines: 89500000
Processed lines: 91000000
Processed lines: 92000000
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Processed lines: 92500000
Processed lines: 93500000
Processed lines: 88000000
Processed lines: 87000000
Processed lines: 92500000
Processed lines: 91500000
Processed lines: 89000000
Processed lines: 94000000
Processed lines: 88500000
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Processed lines: 91500000
Processed lines: 93500000
Processed lines: 90000000
Processed lines: 87500000
Processed lines: 87000000
Processed lines: 93000000
Processed lines: 92000000
Processed lines: 89500000
Finished processing child process. Exiting..
Processed lines: 88000000
Processed lines: 90500000
Processed lines: 89000000
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 90000000
Processed lines: 92500000
Processed lines: 88000000
Processed lines: 93000000
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Processed lines: 88500000
Processed lines: 92000000
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Processed lines: 87500000
Processed lines: 89500000
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 94000000
Processed lines: 92000000
Processed lines: 90500000
Processed lines: 93500000
Processed lines: 88000000
Processed lines: 87500000
Processed lines: 92500000
Processed lines: 90000000
Processed lines: 91000000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 92000000
Processed lines: 91500000
Processed lines: 93000000
Processed lines: 90500000
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Processed lines: 88500000
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Processed lines: 88500000
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Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 89500000
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Processed lines: 92500000
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Finished processing child process. Exiting..
Processed lines: 91000000
Processed lines: 89000000
Processed lines: 90500000
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Processed lines: 91500000
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Finished processing child process. Exiting..
Processed lines: 91000000
Processed lines: 93000000
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Processed lines: 94000000
Processed lines: 89500000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 92500000
Processed lines: 90500000
Processed lines: 92000000
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Processed lines: 90000000
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Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 94000000
Processed lines: 91500000
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Processed lines: 92500000
Processed lines: 90500000
Processed lines: 90500000
Finished processing child process. Exiting..
Processed lines: 92000000
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 90000000
Processed lines: 93000000
Processed lines: 91000000
Processed lines: 92500000
Processed lines: 93500000
Processed lines: 90500000
Processed lines: 90000000
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Processed lines: 94000000
Processed lines: 93000000
Processed lines: 91000000
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Finished processing child process. Exiting..
Processed lines: 92500000
Processed lines: 91500000
Processed lines: 92000000
Processed lines: 90500000
Processed lines: 93500000
Processed lines: 91500000
Processed lines: 93000000
Processed lines: 94000000
Processed lines: 91000000
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Finished processing child process. Exiting..
Processed lines: 91500000
Processed lines: 91500000
Processed lines: 93000000
Processed lines: 92000000
Processed lines: 92500000
Processed lines: 94000000
Processed lines: 91000000
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Processed lines: 93500000
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Finished processing child process. Exiting..
Processed lines: 92000000
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Finished processing child process. Exiting..
Processed lines: 92500000
Processed lines: 93000000
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Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
Processed lines: 92500000
Processed lines: 94000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 93500000
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Processed lines: 94000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 94000000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 94179724 lines in total
Total number of methylation call strings processed: 188359448

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2377770409

Total methylated C's in CpG context:	37346078
Total methylated C's in CHG context:	1784502
Total methylated C's in CHH context:	7425685

Total C to T conversions in CpG context:	268205283
Total C to T conversions in CHG context:	418913612
Total C to T conversions in CHH context:	1644095249

C methylated in CpG context:	12.2%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 16F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_16F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>19F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >19F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 19F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 19F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/19F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/19F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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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: '19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 99571767 lines in total
Total number of methylation call strings processed: 199143534

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2486290912

Total methylated C's in CpG context:	38715437
Total methylated C's in CHG context:	1881993
Total methylated C's in CHH context:	8347696

Total C to T conversions in CpG context:	284892928
Total C to T conversions in CHG context:	443141610
Total C to T conversions in CHH context:	1709311248

C methylated in CpG context:	12.0%
C methylated in non-CpG context:	0.5%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		19F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 19F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 19F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_19F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>22F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >22F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 22F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 22F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/22F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/22F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 66000000
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 66746852 lines in total
Total number of methylation call strings processed: 133493704

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1932255721

Total methylated C's in CpG context:	28515624
Total methylated C's in CHG context:	1366744
Total methylated C's in CHH context:	5635575

Total C to T conversions in CpG context:	210931753
Total C to T conversions in CHG context:	334520859
Total C to T conversions in CHH context:	1351285166

C methylated in CpG context:	11.9%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		22F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 22F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 22F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_22F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>23M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >23M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 23M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 23M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/23M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/23M_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 110649723 lines in total
Total number of methylation call strings processed: 221299446

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2894655837

Total methylated C's in CpG context:	51270609
Total methylated C's in CHG context:	2002961
Total methylated C's in CHH context:	8414346

Total C to T conversions in CpG context:	325736336
Total C to T conversions in CHG context:	516029177
Total C to T conversions in CHH context:	1991202408

C methylated in CpG context:	13.6%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		23M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 23M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 23M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_23M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>29F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >29F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 29F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/29F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/29F_R2_val_2.fq.gz"

Now reading in Bismark result file 29F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Processed lines: 70500000
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Processed lines: 70000000
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Finished processing child process. Exiting..
Processed lines: 68500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 71500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 72000000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 72500000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 72910041 lines in total
Total number of methylation call strings processed: 145820082

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2061199527

Total methylated C's in CpG context:	29672752
Total methylated C's in CHG context:	1416706
Total methylated C's in CHH context:	5937298

Total C to T conversions in CpG context:	228068733
Total C to T conversions in CHG context:	355765857
Total C to T conversions in CHH context:	1440338181

C methylated in CpG context:	11.5%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		29F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 29F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 29F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_29F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>31M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >31M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam


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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 31M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/31M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/31M_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 73000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 76000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 77191386 lines in total
Total number of methylation call strings processed: 154382772

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1930776015

Total methylated C's in CpG context:	34183478
Total methylated C's in CHG context:	1349709
Total methylated C's in CHH context:	5922078

Total C to T conversions in CpG context:	220646744
Total C to T conversions in CHG context:	346999276
Total C to T conversions in CHH context:	1321674730

C methylated in CpG context:	13.4%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		31M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 31M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 31M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_31M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>35F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >35F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam


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Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 35F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/35F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/35F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 81000000
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Finished processing child process. Exiting..
Processed lines: 83500000
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Finished processing child process. Exiting..
Processed lines: 83000000
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Finished processing child process. Exiting..
Processed lines: 82000000
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Finished processing child process. Exiting..
Processed lines: 82000000
Processed lines: 83500000
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Finished processing child process. Exiting..
Processed lines: 78000000
Processed lines: 78000000
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Finished processing child process. Exiting..
Processed lines: 81500000
Processed lines: 82000000
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Finished processing child process. Exiting..
Processed lines: 81000000
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Finished processing child process. Exiting..
Processed lines: 82500000
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Processed lines: 79000000
Processed lines: 81500000
Processed lines: 83000000
Finished processing child process. Exiting..
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 83500000
Finished processing child process. Exiting..
Processed lines: 78500000
Processed lines: 82000000
Processed lines: 83500000
Processed lines: 82500000
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 83000000
Processed lines: 82000000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 83500000
Processed lines: 83000000
Processed lines: 83000000
Finished processing child process. Exiting..
Processed lines: 82500000
Processed lines: 79000000
Processed lines: 83000000
Processed lines: 81000000
Processed lines: 81000000
Processed lines: 81000000
Processed lines: 81000000
Finished processing child process. Exiting..
Processed lines: 83500000
Processed lines: 82500000
Processed lines: 80000000
Processed lines: 80000000
Processed lines: 80000000
Processed lines: 83500000
Processed lines: 83500000
Finished processing child process. Exiting..
Processed lines: 83000000
Processed lines: 83500000
Processed lines: 79500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 83000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 80500000
Finished processing child process. Exiting..
Processed lines: 83500000
Processed lines: 80000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 83500000
Finished processing child process. Exiting..
Processed lines: 81000000
Processed lines: 81000000
Processed lines: 81000000
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 81500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 82000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 82500000
Processed lines: 83000000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 83500000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 83853098 lines in total
Total number of methylation call strings processed: 167706196

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2298440911

Total methylated C's in CpG context:	34690212
Total methylated C's in CHG context:	1663625
Total methylated C's in CHH context:	6720771

Total C to T conversions in CpG context:	254538680
Total C to T conversions in CHG context:	397912346
Total C to T conversions in CHH context:	1602915277

C methylated in CpG context:	12.0%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		35F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 35F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 35F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_35F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>36F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >36F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 36F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/36F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/36F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 85000000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 85207013 lines in total
Total number of methylation call strings processed: 170414026

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2328124966

Total methylated C's in CpG context:	34436105
Total methylated C's in CHG context:	1741368
Total methylated C's in CHH context:	7322382

Total C to T conversions in CpG context:	260760867
Total C to T conversions in CHG context:	405189661
Total C to T conversions in CHH context:	1618674583

C methylated in CpG context:	11.7%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		36F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 36F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 36F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_36F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>39F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >39F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 39F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/39F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/39F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 80000000
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Finished processing child process. Exiting..
Processed lines: 79500000
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Finished processing child process. Exiting..
Processed lines: 79000000
Processed lines: 75500000
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Finished processing child process. Exiting..
Processed lines: 79000000
Processed lines: 79000000
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Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 76000000
Processed lines: 80000000
Processed lines: 75000000
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Finished processing child process. Exiting..
Processed lines: 78500000
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Processed lines: 77000000
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Processed lines: 76500000
Processed lines: 80000000
Processed lines: 76000000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 78500000
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Processed lines: 79500000
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Processed lines: 76000000
Processed lines: 76000000
Processed lines: 80000000
Processed lines: 80000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 76000000
Processed lines: 76000000
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Processed lines: 79500000
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Processed lines: 80000000
Processed lines: 78000000
Processed lines: 76500000
Processed lines: 76500000
Finished processing child process. Exiting..
Processed lines: 76500000
Processed lines: 79000000
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Processed lines: 78000000
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Processed lines: 80000000
Processed lines: 79000000
Processed lines: 80000000
Processed lines: 77500000
Finished processing child process. Exiting..
Processed lines: 78500000
Finished processing child process. Exiting..
Processed lines: 77000000
Processed lines: 77000000
Processed lines: 77000000
Processed lines: 79500000
Processed lines: 78500000
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Processed lines: 77000000
Processed lines: 78000000
Processed lines: 77500000
Processed lines: 78000000
Processed lines: 80000000
Processed lines: 77000000
Processed lines: 78500000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 78000000
Processed lines: 79000000
Processed lines: 77500000
Processed lines: 77500000
Processed lines: 77500000
Processed lines: 80000000
Processed lines: 79000000
Processed lines: 77500000
Processed lines: 77500000
Processed lines: 78500000
Processed lines: 78000000
Finished processing child process. Exiting..
Processed lines: 78500000
Processed lines: 77500000
Processed lines: 79000000
Processed lines: 80000000
Processed lines: 78500000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 78000000
Processed lines: 78000000
Processed lines: 78000000
Processed lines: 79500000
Processed lines: 78000000
Processed lines: 78000000
Processed lines: 79000000
Processed lines: 78500000
Processed lines: 79000000
Processed lines: 79500000
Processed lines: 78000000
Processed lines: 79000000
Processed lines: 80000000
Processed lines: 78500000
Processed lines: 78500000
Processed lines: 78500000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 79500000
Processed lines: 78500000
Processed lines: 78500000
Processed lines: 79000000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 80000000
Processed lines: 78500000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 79000000
Processed lines: 79000000
Processed lines: 79000000
Processed lines: 80000000
Processed lines: 79000000
Processed lines: 79500000
Processed lines: 79000000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 79000000
Finished processing child process. Exiting..
Processed lines: 80000000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 80000000
Processed lines: 79500000
Finished processing child process. Exiting..
Processed lines: 79500000
Processed lines: 80000000
Processed lines: 80000000
Processed lines: 80000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 80000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 80000000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 80072194 lines in total
Total number of methylation call strings processed: 160144388

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2074276116

Total methylated C's in CpG context:	31536948
Total methylated C's in CHG context:	1496914
Total methylated C's in CHH context:	6317241

Total C to T conversions in CpG context:	233554310
Total C to T conversions in CHG context:	362416138
Total C to T conversions in CHH context:	1438954565

C methylated in CpG context:	11.9%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		39F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 39F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 39F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_39F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>3F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >3F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 3F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 3F_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 3F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/3F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/3F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 84500000
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Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 86601366 lines in total
Total number of methylation call strings processed: 173202732

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2245598302

Total methylated C's in CpG context:	33278296
Total methylated C's in CHG context:	1581182
Total methylated C's in CHH context:	6889997

Total C to T conversions in CpG context:	258732657
Total C to T conversions in CHG context:	397571420
Total C to T conversions in CHH context:	1547544750

C methylated in CpG context:	11.4%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		3F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 3F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 3F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_3F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>41F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >41F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 41F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/41F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/41F_R2_val_2.fq.gz"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 56050400 lines in total
Total number of methylation call strings processed: 112100800

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1402364113

Total methylated C's in CpG context:	21603092
Total methylated C's in CHG context:	1050441
Total methylated C's in CHH context:	4458912

Total C to T conversions in CpG context:	158790370
Total C to T conversions in CHG context:	248626025
Total C to T conversions in CHH context:	967835273

C methylated in CpG context:	12.0%
C methylated in non-CpG context:	0.5%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		41F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 41F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 41F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_41F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>44F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >44F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam


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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 44F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/44F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/44F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 150500000
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 157156371 lines in total
Total number of methylation call strings processed: 314312742

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	4359634563

Total methylated C's in CpG context:	62164671
Total methylated C's in CHG context:	2974806
Total methylated C's in CHH context:	12301418

Total C to T conversions in CpG context:	486787004
Total C to T conversions in CHG context:	754995811
Total C to T conversions in CHH context:	3040410853

C methylated in CpG context:	11.3%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		44F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 44F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 44F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_44F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>48M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >48M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/48M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/48M_R2_val_2.fq.gz"

Now reading in Bismark result file 48M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Finished processing child process. Exiting..
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Processed lines: 96500000
Processed lines: 96500000
Processed lines: 103500000
Processed lines: 99500000
Finished processing child process. Exiting..
Processed lines: 101500000
Processed lines: 103500000
Processed lines: 100000000
Processed lines: 102500000
Finished processing child process. Exiting..
Processed lines: 99500000
Processed lines: 102000000
Processed lines: 100000000
Processed lines: 100500000
Processed lines: 101000000
Processed lines: 102000000
Processed lines: 97000000
Processed lines: 97000000
Processed lines: 97000000
Processed lines: 97000000
Processed lines: 103500000
Processed lines: 96500000
Processed lines: 97000000
Processed lines: 96500000
Processed lines: 102500000
Finished processing child process. Exiting..
Processed lines: 102000000
Processed lines: 98500000
Processed lines: 101500000
Processed lines: 101000000
Processed lines: 97000000
Processed lines: 97000000
Processed lines: 100000000
Processed lines: 102000000
Processed lines: 100500000
Processed lines: 103000000
Processed lines: 100000000
Processed lines: 102500000
Processed lines: 101000000
Processed lines: 100500000
Processed lines: 101500000
Processed lines: 102500000
Processed lines: 97500000
Processed lines: 97500000
Processed lines: 97500000
Processed lines: 97500000
Processed lines: 103000000
Processed lines: 97500000
Processed lines: 97000000
Processed lines: 97000000
Processed lines: 102500000
Processed lines: 102000000
Processed lines: 101500000
Processed lines: 99000000
Processed lines: 100500000
Processed lines: 97500000
Processed lines: 97500000
Processed lines: 102500000
Processed lines: 101000000
Processed lines: 103500000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 103000000
Processed lines: 101500000
Processed lines: 101000000
Processed lines: 102000000
Processed lines: 103500000
Processed lines: 98000000
Processed lines: 98000000
Processed lines: 98000000
Processed lines: 103000000
Processed lines: 98000000
Processed lines: 98000000
Finished processing child process. Exiting..
Processed lines: 97500000
Processed lines: 97500000
Processed lines: 103000000
Processed lines: 102500000
Processed lines: 102000000
Processed lines: 101000000
Processed lines: 99500000
Processed lines: 103000000
Processed lines: 98000000
Processed lines: 98000000
Processed lines: 101500000
Processed lines: 101000000
Processed lines: 103500000
Processed lines: 102000000
Finished processing child process. Exiting..
Processed lines: 101500000
Processed lines: 102500000
Processed lines: 98500000
Processed lines: 98500000
Processed lines: 98500000
Processed lines: 98500000
Processed lines: 98500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 98000000
Processed lines: 98000000
Processed lines: 103000000
Processed lines: 102500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 101500000
Processed lines: 103500000
Processed lines: 100000000
Finished processing child process. Exiting..
Processed lines: 98500000
Processed lines: 98500000
Processed lines: 102000000
Processed lines: 101500000
Processed lines: 102500000
Processed lines: 103000000
Processed lines: 102000000
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 103500000
Processed lines: 103000000
Processed lines: 98500000
Processed lines: 98500000
Finished processing child process. Exiting..
Processed lines: 102000000
Processed lines: 100500000
Processed lines: 102500000
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 102000000
Processed lines: 103000000
Processed lines: 103500000
Processed lines: 102500000
Finished processing child process. Exiting..
Processed lines: 103500000
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 99500000
Finished processing child process. Exiting..
Processed lines: 99000000
Processed lines: 99000000
Processed lines: 102500000
Processed lines: 103000000
Processed lines: 101000000
Processed lines: 102500000
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 103500000
Finished processing child process. Exiting..
Processed lines: 103000000
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 103000000
Processed lines: 99500000
Processed lines: 99500000
Processed lines: 103500000
Finished processing child process. Exiting..
Processed lines: 101500000
Processed lines: 103000000
Processed lines: 103500000
Processed lines: 100000000
Processed lines: 100000000
Finished processing child process. Exiting..
Processed lines: 103500000
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 100500000
Finished processing child process. Exiting..
Processed lines: 100000000
Processed lines: 100000000
Processed lines: 102000000
Processed lines: 103500000
Finished processing child process. Exiting..
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 100500000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 102500000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101000000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 103000000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 101500000
Processed lines: 103500000
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102000000
Finished processing child process. Exiting..
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102000000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 102500000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103000000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Processed lines: 103500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 103543900 lines in total
Total number of methylation call strings processed: 207087800

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2570349030

Total methylated C's in CpG context:	46430852
Total methylated C's in CHG context:	1955189
Total methylated C's in CHH context:	9333350

Total C to T conversions in CpG context:	302893637
Total C to T conversions in CHG context:	487842570
Total C to T conversions in CHH context:	1721893432

C methylated in CpG context:	13.3%
C methylated in non-CpG context:	0.5%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		48M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 48M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 48M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_48M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>50F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >50F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 50F_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 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 50F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/50F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/50F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 72500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 76500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 75500000
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Finished processing child process. Exiting..
Processed lines: 75000000
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Finished processing child process. Exiting..
Processed lines: 72500000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 73500000
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Finished processing child process. Exiting..
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Processed lines: 76500000
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Finished processing child process. Exiting..
Processed lines: 74000000
Processed lines: 74000000
Processed lines: 76500000
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Processed lines: 73500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 76500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 74500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 75500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 76500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 76725340 lines in total
Total number of methylation call strings processed: 153450680

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2234334784

Total methylated C's in CpG context:	33203460
Total methylated C's in CHG context:	1600748
Total methylated C's in CHH context:	6728111

Total C to T conversions in CpG context:	244518398
Total C to T conversions in CHG context:	386893249
Total C to T conversions in CHH context:	1561390818

C methylated in CpG context:	12.0%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		50F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 50F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 50F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_50F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>52F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >52F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 52F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 52F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/52F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/52F_R2_val_2.fq.gz"
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Processed lines: 81000000
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 83000000
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Processed lines: 83000000
Processed lines: 88500000
Processed lines: 90000000
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Processed lines: 82000000
Processed lines: 82000000
Processed lines: 82000000
Finished processing child process. Exiting..
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 85500000
Processed lines: 88000000
Processed lines: 87000000
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 86500000
Processed lines: 88500000
Processed lines: 85000000
Processed lines: 82500000
Processed lines: 85500000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 81500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 88000000
Processed lines: 89000000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 88500000
Processed lines: 87500000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 82500000
Processed lines: 82500000
Processed lines: 82500000
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Processed lines: 86000000
Processed lines: 89500000
Processed lines: 88000000
Processed lines: 89000000
Processed lines: 87000000
Processed lines: 85500000
Processed lines: 86000000
Processed lines: 83000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 90000000
Processed lines: 82000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 88000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 86500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 83000000
Processed lines: 90000000
Processed lines: 83000000
Processed lines: 83000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 87500000
Processed lines: 86000000
Processed lines: 86500000
Processed lines: 83500000
Processed lines: 82500000
Processed lines: 89000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 88500000
Processed lines: 87000000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 83500000
Processed lines: 89000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 88000000
Processed lines: 86500000
Processed lines: 87000000
Processed lines: 84000000
Processed lines: 89500000
Processed lines: 83000000
Processed lines: 90000000
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 87500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 85000000
Processed lines: 85000000
Processed lines: 85000000
Processed lines: 89500000
Processed lines: 84000000
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Processed lines: 84000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 88500000
Processed lines: 87000000
Processed lines: 87500000
Processed lines: 84500000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 83500000
Processed lines: 89500000
Processed lines: 88000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 87500000
Processed lines: 88000000
Processed lines: 85000000
Processed lines: 84000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 89500000
Processed lines: 88000000
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Processed lines: 85000000
Processed lines: 85000000
Processed lines: 88500000
Processed lines: 85500000
Processed lines: 84500000
Processed lines: 89000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 90000000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 89000000
Processed lines: 85500000
Processed lines: 89500000
Processed lines: 86000000
Processed lines: 85000000
Processed lines: 89000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 89500000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 86500000
Processed lines: 85500000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Finished processing child process. Exiting..
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87000000
Processed lines: 86000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 87500000
Processed lines: 86500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 87000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 87500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 88000000
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 90000000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 90021414 lines in total
Total number of methylation call strings processed: 180042828

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2568366686

Total methylated C's in CpG context:	37267533
Total methylated C's in CHG context:	1750935
Total methylated C's in CHH context:	7241846

Total C to T conversions in CpG context:	280880651
Total C to T conversions in CHG context:	440074373
Total C to T conversions in CHH context:	1801151348

C methylated in CpG context:	11.7%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		52F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 52F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 52F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_52F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>53F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >53F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_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 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_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 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_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 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 53F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/53F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/53F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 88500000
Processed lines: 88000000
Processed lines: 89000000
Processed lines: 86000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 84000000
Processed lines: 87000000
Processed lines: 89500000
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 83500000
Processed lines: 87000000
Processed lines: 90000000
Processed lines: 88500000
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 83000000
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 84500000
Processed lines: 86500000
Processed lines: 84500000
Processed lines: 90000000
Processed lines: 87500000
Finished processing child process. Exiting..
Processed lines: 87500000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 84000000
Processed lines: 88000000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 90000000
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 83500000
Processed lines: 85000000
Processed lines: 85000000
Processed lines: 88000000
Processed lines: 85000000
Processed lines: 87000000
Processed lines: 85000000
Processed lines: 88000000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 88500000
Processed lines: 84500000
Processed lines: 90000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 88500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 85500000
Processed lines: 87500000
Processed lines: 84000000
Processed lines: 88500000
Processed lines: 90000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 85000000
Finished processing child process. Exiting..
Processed lines: 90000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 89000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 86000000
Processed lines: 84500000
Processed lines: 88000000
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 85500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 86500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 85000000
Processed lines: 90000000
Processed lines: 88500000
Processed lines: 89500000
Processed lines: 86000000
Processed lines: 90000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Processed lines: 87000000
Finished processing child process. Exiting..
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 85500000
Processed lines: 89000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 86500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 86000000
Processed lines: 89500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 87000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 90000000
Processed lines: 86500000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 87000000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 88000000
Processed lines: 87500000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 88000000
Processed lines: 88500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 88500000
Processed lines: 89000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 90000000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 90488807 lines in total
Total number of methylation call strings processed: 180977614

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2495589632

Total methylated C's in CpG context:	36895767
Total methylated C's in CHG context:	1730940
Total methylated C's in CHH context:	7042696

Total C to T conversions in CpG context:	273790381
Total C to T conversions in CHG context:	429246884
Total C to T conversions in CHH context:	1746882964

C methylated in CpG context:	11.9%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		53F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 53F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 53F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_53F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>54F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >54F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 54F_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 54F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 54F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/54F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/54F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 91500000
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Processed lines: 90500000
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Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 91500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 94000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 94000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
Processed lines: 93500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 94455697 lines in total
Total number of methylation call strings processed: 188911394

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2648996482

Total methylated C's in CpG context:	39062781
Total methylated C's in CHG context:	1817935
Total methylated C's in CHH context:	7450923

Total C to T conversions in CpG context:	291237285
Total C to T conversions in CHG context:	459726104
Total C to T conversions in CHH context:	1849701454

C methylated in CpG context:	11.8%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		54F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 54F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 54F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_54F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>59M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >59M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 59M_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 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 59M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/59M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/59M_R2_val_2.fq.gz"
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Processed lines: 71000000
Processed lines: 66500000
Processed lines: 70500000
Processed lines: 69500000
Processed lines: 68000000
Processed lines: 70000000
Processed lines: 70000000
Processed lines: 69000000
Processed lines: 68000000
Processed lines: 71000000
Processed lines: 68500000
Processed lines: 70000000
Processed lines: 67000000
Processed lines: 70500000
Processed lines: 67000000
Processed lines: 71500000
Processed lines: 67500000
Processed lines: 68500000
Processed lines: 69500000
Processed lines: 67500000
Processed lines: 72000000
Processed lines: 67000000
Processed lines: 67000000
Processed lines: 68000000
Processed lines: 67500000
Processed lines: 70500000
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 69500000
Processed lines: 67000000
Processed lines: 71000000
Processed lines: 70000000
Processed lines: 68500000
Processed lines: 70500000
Processed lines: 70500000
Processed lines: 69500000
Processed lines: 68500000
Processed lines: 71500000
Processed lines: 70500000
Processed lines: 71000000
Processed lines: 69000000
Processed lines: 72000000
Processed lines: 67500000
Processed lines: 67500000
Processed lines: 68000000
Processed lines: 69000000
Processed lines: 70000000
Processed lines: 72500000
Processed lines: 68000000
Processed lines: 68500000
Processed lines: 67500000
Processed lines: 67500000
Processed lines: 71000000
Processed lines: 68000000
Processed lines: 72000000
Processed lines: 72000000
Processed lines: 70000000
Processed lines: 70500000
Processed lines: 67500000
Processed lines: 69000000
Processed lines: 71500000
Processed lines: 71000000
Processed lines: 71000000
Processed lines: 70000000
Processed lines: 69000000
Processed lines: 72000000
Processed lines: 71000000
Processed lines: 71500000
Processed lines: 69500000
Processed lines: 72500000
Processed lines: 68000000
Processed lines: 68500000
Processed lines: 68000000
Processed lines: 69500000
Processed lines: 73000000
Processed lines: 70500000
Processed lines: 68500000
Processed lines: 69000000
Processed lines: 71500000
Processed lines: 70500000
Processed lines: 68000000
Processed lines: 68000000
Processed lines: 68500000
Processed lines: 72500000
Processed lines: 72500000
Processed lines: 71000000
Processed lines: 68000000
Processed lines: 69500000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 70500000
Processed lines: 72500000
Processed lines: 69500000
Processed lines: 72000000
Processed lines: 71500000
Processed lines: 70000000
Processed lines: 73000000
Processed lines: 68500000
Processed lines: 69000000
Processed lines: 68500000
Processed lines: 70000000
Processed lines: 71000000
Processed lines: 69000000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 69500000
Processed lines: 71000000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 69000000
Processed lines: 68500000
Processed lines: 68500000
Processed lines: 71500000
Processed lines: 70000000
Processed lines: 68500000
Processed lines: 72000000
Processed lines: 72500000
Processed lines: 72000000
Processed lines: 71000000
Processed lines: 73000000
Processed lines: 72500000
Processed lines: 70000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 70500000
Processed lines: 72000000
Processed lines: 69500000
Processed lines: 69000000
Processed lines: 69000000
Processed lines: 71500000
Processed lines: 70500000
Finished processing child process. Exiting..
Processed lines: 69500000
Processed lines: 72500000
Processed lines: 71500000
Processed lines: 70000000
Processed lines: 69500000
Processed lines: 72000000
Processed lines: 69000000
Processed lines: 69000000
Processed lines: 70500000
Processed lines: 69000000
Processed lines: 72500000
Processed lines: 73000000
Processed lines: 72500000
Processed lines: 71500000
Processed lines: 70500000
Processed lines: 73000000
Processed lines: 71000000
Processed lines: 72500000
Processed lines: 70000000
Processed lines: 69500000
Processed lines: 69500000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 71000000
Processed lines: 70000000
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 70500000
Processed lines: 72000000
Processed lines: 70000000
Processed lines: 72500000
Processed lines: 71000000
Processed lines: 69500000
Processed lines: 69500000
Processed lines: 69500000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 71000000
Processed lines: 71500000
Processed lines: 73000000
Processed lines: 70500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 70000000
Processed lines: 70000000
Processed lines: 72500000
Processed lines: 70500000
Processed lines: 71500000
Processed lines: 72500000
Processed lines: 71000000
Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 70500000
Processed lines: 71500000
Processed lines: 70000000
Processed lines: 70000000
Processed lines: 70000000
Processed lines: 72500000
Processed lines: 71500000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 71000000
Processed lines: 73000000
Processed lines: 70500000
Processed lines: 70500000
Processed lines: 71000000
Processed lines: 71500000
Processed lines: 72000000
Processed lines: 73000000
Processed lines: 71000000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 70500000
Processed lines: 70500000
Processed lines: 70500000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 71500000
Finished processing child process. Exiting..
Processed lines: 71000000
Processed lines: 71000000
Processed lines: 72000000
Processed lines: 72500000
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 72500000
Processed lines: 72500000
Processed lines: 73000000
Processed lines: 71000000
Processed lines: 71000000
Processed lines: 71000000
Processed lines: 72000000
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 72500000
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 72000000
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 71500000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 73000000
Processed lines: 72500000
Processed lines: 72500000
Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 72000000
Processed lines: 72000000
Processed lines: 72000000
Processed lines: 72500000
Processed lines: 72500000
Processed lines: 73000000
Processed lines: 73000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 72500000
Processed lines: 72500000
Processed lines: 73000000
Processed lines: 73000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 73000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 73233985 lines in total
Total number of methylation call strings processed: 146467970

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1689141290

Total methylated C's in CpG context:	31866013
Total methylated C's in CHG context:	1219594
Total methylated C's in CHH context:	5167236

Total C to T conversions in CpG context:	194609831
Total C to T conversions in CHG context:	309497248
Total C to T conversions in CHH context:	1146781368

C methylated in CpG context:	14.1%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		59M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 59M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 59M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_59M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>64M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >64M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 64M_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 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 64M_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/64M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/64M_R2_val_2.fq.gz"

Now reading in Bismark result file 64M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Processed lines: 85500000
Processed lines: 86500000
Processed lines: 88000000
Processed lines: 85000000
Processed lines: 90000000
Processed lines: 85500000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 88000000
Processed lines: 85500000
Processed lines: 85000000
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Processed lines: 90000000
Processed lines: 88500000
Processed lines: 90500000
Processed lines: 87500000
Processed lines: 86000000
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 86500000
Processed lines: 85000000
Processed lines: 85500000
Processed lines: 86500000
Processed lines: 87500000
Processed lines: 91000000
Processed lines: 90000000
Processed lines: 89000000
Processed lines: 87000000
Processed lines: 88500000
Processed lines: 86000000
Processed lines: 85500000
Processed lines: 90500000
Processed lines: 85500000
Processed lines: 89500000
Processed lines: 91000000
Processed lines: 86000000
Processed lines: 88500000
Processed lines: 90500000
Processed lines: 87500000
Processed lines: 85500000
Processed lines: 86000000
Processed lines: 91000000
Processed lines: 89000000
Processed lines: 88000000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 86500000
Processed lines: 87000000
Processed lines: 91500000
Processed lines: 85500000
Processed lines: 90500000
Processed lines: 86000000
Processed lines: 87000000
Processed lines: 88000000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 86500000
Processed lines: 91000000
Processed lines: 86000000
Processed lines: 91500000
Processed lines: 90000000
Processed lines: 86000000
Processed lines: 86500000
Processed lines: 89000000
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 88000000
Processed lines: 86000000
Processed lines: 89500000
Processed lines: 86500000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 90000000
Processed lines: 87000000
Processed lines: 87500000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 86000000
Processed lines: 86500000
Processed lines: 90000000
Processed lines: 87500000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 88000000
Processed lines: 87000000
Processed lines: 86500000
Processed lines: 90500000
Finished processing child process. Exiting..
Processed lines: 86500000
Processed lines: 87000000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 88500000
Processed lines: 90000000
Processed lines: 86500000
Processed lines: 87000000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 87500000
Processed lines: 88000000
Processed lines: 91500000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 87000000
Processed lines: 86500000
Processed lines: 88000000
Processed lines: 90000000
Processed lines: 88500000
Processed lines: 87500000
Processed lines: 91000000
Processed lines: 87000000
Finished processing child process. Exiting..
Processed lines: 87000000
Processed lines: 87500000
Processed lines: 90000000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 87000000
Processed lines: 87500000
Processed lines: 89500000
Finished processing child process. Exiting..
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 88000000
Processed lines: 88500000
Processed lines: 91000000
Processed lines: 89500000
Processed lines: 87500000
Processed lines: 87000000
Processed lines: 88500000
Processed lines: 90500000
Processed lines: 89000000
Processed lines: 91500000
Processed lines: 88000000
Processed lines: 87500000
Processed lines: 87500000
Processed lines: 88000000
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 89500000
Finished processing child process. Exiting..
Processed lines: 88000000
Processed lines: 90000000
Processed lines: 87500000
Processed lines: 91500000
Processed lines: 88500000
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 91500000
Processed lines: 90000000
Processed lines: 91000000
Processed lines: 88000000
Processed lines: 89000000
Processed lines: 87500000
Processed lines: 89500000
Processed lines: 88500000
Processed lines: 88000000
Processed lines: 88000000
Processed lines: 88500000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 90000000
Processed lines: 91500000
Processed lines: 90500000
Processed lines: 88000000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 88500000
Processed lines: 88000000
Processed lines: 90000000
Processed lines: 89000000
Finished processing child process. Exiting..
Processed lines: 88500000
Processed lines: 88500000
Processed lines: 89000000
Processed lines: 91500000
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 89000000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 91000000
Processed lines: 90000000
Processed lines: 89000000
Processed lines: 90500000
Processed lines: 88500000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 89000000
Processed lines: 89500000
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 89000000
Processed lines: 90000000
Processed lines: 90500000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 89000000
Processed lines: 90000000
Finished processing child process. Exiting..
Processed lines: 89500000
Processed lines: 89500000
Processed lines: 90000000
Processed lines: 91500000
Processed lines: 90000000
Processed lines: 89500000
Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 90000000
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 89500000
Processed lines: 90500000
Finished processing child process. Exiting..
Processed lines: 90000000
Processed lines: 90000000
Processed lines: 90500000
Processed lines: 90500000
Processed lines: 90000000
Processed lines: 91000000
Processed lines: 91500000
Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 91500000
Processed lines: 91000000
Processed lines: 90000000
Processed lines: 90500000
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 91500000
Finished processing child process. Exiting..
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 90500000
Processed lines: 91000000
Processed lines: 91000000
Processed lines: 91500000
Finished processing child process. Exiting..
Processed lines: 91500000
Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 91500000
Finished processing child process. Exiting..
Processed lines: 91000000
Processed lines: 91500000
Processed lines: 91500000
Finished processing child process. Exiting..
Processed lines: 91500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 91500000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 91896803 lines in total
Total number of methylation call strings processed: 183793606

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2479740246

Total methylated C's in CpG context:	42206303
Total methylated C's in CHG context:	1779052
Total methylated C's in CHH context:	7273814

Total C to T conversions in CpG context:	276397190
Total C to T conversions in CHG context:	438750654
Total C to T conversions in CHH context:	1713333233

C methylated in CpG context:	13.2%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		64M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 64M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 64M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_64M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>6M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >6M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_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 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 6M_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 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/6M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/6M_R2_val_2.fq.gz"

Now reading in Bismark result file 6M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 79000000
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Finished processing child process. Exiting..
Processed lines: 76500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 79500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 77500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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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: '6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 80219444 lines in total
Total number of methylation call strings processed: 160438888

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1995315281

Total methylated C's in CpG context:	36932556
Total methylated C's in CHG context:	1621071
Total methylated C's in CHH context:	7648031

Total C to T conversions in CpG context:	241004510
Total C to T conversions in CHG context:	379429880
Total C to T conversions in CHH context:	1328679233

C methylated in CpG context:	13.3%
C methylated in non-CpG context:	0.5%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		6M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 6M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 6M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_6M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>76F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >76F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 76F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/76F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/76F_R2_val_2.fq.gz"
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Finished processing child process. Exiting..
Processed lines: 82500000
Processed lines: 81500000
Processed lines: 81000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 77000000
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Processed lines: 80500000
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Processed lines: 78000000
Processed lines: 79500000
Processed lines: 80000000
Finished processing child process. Exiting..
Processed lines: 77500000
Processed lines: 82000000
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Processed lines: 81500000
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Processed lines: 78000000
Processed lines: 81000000
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Processed lines: 80500000
Finished processing child process. Exiting..
Processed lines: 81500000
Processed lines: 82000000
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Processed lines: 77500000
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Processed lines: 81000000
Processed lines: 78500000
Processed lines: 80000000
Processed lines: 80500000
Processed lines: 82500000
Processed lines: 78000000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82000000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 81500000
Processed lines: 78000000
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Processed lines: 78500000
Processed lines: 81000000
Processed lines: 82000000
Processed lines: 82500000
Processed lines: 79500000
Processed lines: 80000000
Finished processing child process. Exiting..
Processed lines: 78000000
Processed lines: 80000000
Processed lines: 81500000
Processed lines: 79000000
Processed lines: 81000000
Processed lines: 80500000
Processed lines: 79000000
Processed lines: 78500000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 82000000
Processed lines: 78500000
Processed lines: 79500000
Processed lines: 79000000
Processed lines: 81500000
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Processed lines: 79000000
Processed lines: 82500000
Processed lines: 80000000
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 78500000
Processed lines: 80500000
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Processed lines: 82500000
Processed lines: 81000000
Processed lines: 79000000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 82000000
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 79500000
Processed lines: 80500000
Processed lines: 81000000
Processed lines: 79000000
Processed lines: 81000000
Processed lines: 82500000
Processed lines: 80000000
Processed lines: 82000000
Processed lines: 81500000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 79500000
Processed lines: 81500000
Processed lines: 82500000
Processed lines: 80500000
Processed lines: 79500000
Processed lines: 80000000
Processed lines: 80000000
Processed lines: 80000000
Finished processing child process. Exiting..
Processed lines: 81000000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 79500000
Processed lines: 80500000
Processed lines: 82500000
Processed lines: 82000000
Processed lines: 80500000
Finished processing child process. Exiting..
Processed lines: 80000000
Processed lines: 82000000
Processed lines: 80000000
Processed lines: 81000000
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 80500000
Processed lines: 81500000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 80000000
Processed lines: 81000000
Processed lines: 82500000
Processed lines: 81000000
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 82500000
Processed lines: 81500000
Finished processing child process. Exiting..
Processed lines: 80500000
Processed lines: 81000000
Processed lines: 81000000
Processed lines: 81000000
Processed lines: 82000000
Processed lines: 82500000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 80500000
Finished processing child process. Exiting..
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81000000
Processed lines: 82000000
Processed lines: 81000000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 81000000
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 81500000
Processed lines: 81500000
Processed lines: 82000000
Processed lines: 82500000
Processed lines: 82000000
Processed lines: 82000000
Finished processing child process. Exiting..
Processed lines: 81500000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82000000
Processed lines: 82000000
Processed lines: 82500000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 82000000
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82500000
Finished processing child process. Exiting..
Processed lines: 82500000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 82560622 lines in total
Total number of methylation call strings processed: 165121244

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2243661587

Total methylated C's in CpG context:	34487480
Total methylated C's in CHG context:	1538367
Total methylated C's in CHH context:	6745430

Total C to T conversions in CpG context:	252523035
Total C to T conversions in CHG context:	397100054
Total C to T conversions in CHH context:	1551267221

C methylated in CpG context:	12.0%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		76F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 76F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 76F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_76F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>77F_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >77F_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 77F_R1_val_1_bismark_bt2_pe.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 77F_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/77F_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/77F_R2_val_2.fq.gz"
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Processed lines: 88500000
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Processed lines: 90000000
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Processed lines: 92500000
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Processed lines: 91500000
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Processed lines: 90000000
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Processed lines: 91000000
Processed lines: 89500000
Processed lines: 92500000
Processed lines: 88500000
Processed lines: 90000000
Processed lines: 91500000
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Processed lines: 89000000
Processed lines: 94500000
Processed lines: 93000000
Processed lines: 89500000
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Processed lines: 91500000
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Processed lines: 95000000
Processed lines: 93500000
Processed lines: 92500000
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Finished processing child process. Exiting..
Processed lines: 90500000
Processed lines: 94500000
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Processed lines: 91000000
Finished processing child process. Exiting..
Processed lines: 94500000
Processed lines: 91500000
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Processed lines: 90000000
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Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
Processed lines: 92500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 90500000
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Finished processing child process. Exiting..
Processed lines: 94000000
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Processed lines: 90500000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 94500000
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Finished processing child process. Exiting..
Processed lines: 92000000
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Processed lines: 93500000
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Finished processing child process. Exiting..
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Processed lines: 94500000
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Processed lines: 95000000
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Finished processing child process. Exiting..
Processed lines: 92500000
Processed lines: 94500000
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Processed lines: 93500000
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Finished processing child process. Exiting..
Processed lines: 94000000
Processed lines: 93000000
Processed lines: 92500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Processed lines: 93000000
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Finished processing child process. Exiting..
Processed lines: 94500000
Processed lines: 94000000
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Finished processing child process. Exiting..
Processed lines: 93500000
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Finished processing child process. Exiting..
Processed lines: 93500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 95000000
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 95462715 lines in total
Total number of methylation call strings processed: 190925430

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2499600963

Total methylated C's in CpG context:	36760446
Total methylated C's in CHG context:	1702958
Total methylated C's in CHH context:	7092183

Total C to T conversions in CpG context:	283258341
Total C to T conversions in CHG context:	441615989
Total C to T conversions in CHH context:	1729171046

C methylated in CpG context:	11.5%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		77F_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 77F_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 77F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_77F_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>7M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >7M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 7M_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 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 7M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 7M_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 7M_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/7M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/7M_R2_val_2.fq.gz"
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Processed lines: 72500000
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Processed lines: 70000000
Processed lines: 67500000
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Processed lines: 71500000
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Processed lines: 73500000
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Processed lines: 72500000
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Processed lines: 73500000
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Processed lines: 71500000
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Processed lines: 71000000
Processed lines: 73500000
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Processed lines: 72000000
Processed lines: 73500000
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Processed lines: 72500000
Processed lines: 74500000
Processed lines: 74000000
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Processed lines: 73000000
Processed lines: 71500000
Processed lines: 72000000
Processed lines: 69500000
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Processed lines: 71000000
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Processed lines: 69000000
Processed lines: 74500000
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Processed lines: 72000000
Processed lines: 70000000
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Processed lines: 70500000
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Processed lines: 73500000
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Processed lines: 71000000
Processed lines: 72500000
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Processed lines: 74500000
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Processed lines: 73000000
Processed lines: 71000000
Processed lines: 73500000
Processed lines: 72000000
Processed lines: 72500000
Processed lines: 75000000
Processed lines: 71500000
Processed lines: 70000000
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Processed lines: 69500000
Processed lines: 72500000
Processed lines: 69500000
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Processed lines: 70500000
Processed lines: 74500000
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Processed lines: 71000000
Processed lines: 72000000
Processed lines: 74500000
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Processed lines: 73000000
Processed lines: 71500000
Processed lines: 75000000
Processed lines: 74500000
Processed lines: 75500000
Processed lines: 73500000
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Processed lines: 71500000
Processed lines: 74000000
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Processed lines: 72500000
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Processed lines: 72000000
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Processed lines: 70000000
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Processed lines: 70500000
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Processed lines: 71000000
Processed lines: 71000000
Processed lines: 71500000
Processed lines: 75000000
Processed lines: 72500000
Processed lines: 74500000
Processed lines: 73500000
Processed lines: 72000000
Finished processing child process. Exiting..
Processed lines: 75500000
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Finished processing child process. Exiting..
Processed lines: 73500000
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Processed lines: 72500000
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Finished processing child process. Exiting..
Processed lines: 72500000
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Finished processing child process. Exiting..
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 74000000
Processed lines: 71000000
Processed lines: 75500000
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Processed lines: 72500000
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Processed lines: 73500000
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Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 75000000
Processed lines: 75500000
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Finished processing child process. Exiting..
Processed lines: 74500000
Processed lines: 74000000
Processed lines: 73000000
Processed lines: 71500000
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Processed lines: 72500000
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Processed lines: 72000000
Processed lines: 73500000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 75000000
Processed lines: 73500000
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Processed lines: 75500000
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Processed lines: 72000000
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Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 74000000
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Processed lines: 72500000
Processed lines: 72500000
Processed lines: 75500000
Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 74000000
Processed lines: 74500000
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Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 74000000
Processed lines: 74500000
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Processed lines: 72500000
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Processed lines: 73000000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 74500000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 74500000
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Processed lines: 73500000
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Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 75500000
Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 75500000
Processed lines: 74500000
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Processed lines: 74000000
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Finished processing child process. Exiting..
Processed lines: 75500000
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Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 74000000
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Finished processing child process. Exiting..
Processed lines: 74500000
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Finished processing child process. Exiting..
Processed lines: 75500000
Processed lines: 74500000
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Processed lines: 74500000
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Processed lines: 75000000
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Finished processing child process. Exiting..
Processed lines: 75000000
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Finished processing child process. Exiting..
Processed lines: 75000000
Processed lines: 75000000
Processed lines: 75500000
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Processed lines: 75500000
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: '7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 75968903 lines in total
Total number of methylation call strings processed: 151937806

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2148117321

Total methylated C's in CpG context:	38122812
Total methylated C's in CHG context:	1485354
Total methylated C's in CHH context:	6163716

Total C to T conversions in CpG context:	236284094
Total C to T conversions in CHG context:	381726093
Total C to T conversions in CHH context:	1484335252

C methylated in CpG context:	13.9%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		7M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 7M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 7M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_7M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>9M_R1_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...


Now testing Bismark result file >9M_R1_val_1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...)	...passed!
Writing result file containing methylation information for C in CpG context to CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in any other context to Non_CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file 9M_R1_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file 9M_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:v0.22.3	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cvirg/9M_R1_val_1.fq.gz -2 /gscratch/srlab/sr320/data/cvirg/9M_R2_val_2.fq.gz"
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Processed lines: 70000000
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Processed lines: 69500000
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Processed lines: 68500000
Processed lines: 70000000
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Processed lines: 69500000
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Processed lines: 71500000
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Processed lines: 70000000
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Processed lines: 70500000
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Processed lines: 71500000
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Processed lines: 67500000
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Processed lines: 69000000
Processed lines: 69500000
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Processed lines: 72500000
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Processed lines: 72000000
Processed lines: 68000000
Processed lines: 70000000
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Processed lines: 70500000
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Processed lines: 72000000
Processed lines: 71500000
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Processed lines: 67500000
Processed lines: 68500000
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Processed lines: 71000000
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Processed lines: 70500000
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Processed lines: 68000000
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Processed lines: 70000000
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Processed lines: 71500000
Processed lines: 69500000
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Processed lines: 71500000
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Processed lines: 72500000
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Processed lines: 70000000
Finished processing child process. Exiting..
Processed lines: 68000000
Processed lines: 71500000
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Processed lines: 73000000
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Processed lines: 68500000
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Processed lines: 73000000
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Processed lines: 70000000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 73000000
Processed lines: 71500000
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Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 68500000
Processed lines: 69500000
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Processed lines: 73000000
Processed lines: 71500000
Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 72500000
Processed lines: 71000000
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Processed lines: 71500000
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Processed lines: 69500000
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Finished processing child process. Exiting..
Processed lines: 72000000
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Processed lines: 72500000
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Finished processing child process. Exiting..
Processed lines: 69500000
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Processed lines: 72500000
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Finished processing child process. Exiting..
Processed lines: 71500000
Processed lines: 73000000
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Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 69500000
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Processed lines: 72500000
Processed lines: 70000000
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Finished processing child process. Exiting..
Processed lines: 73000000
Processed lines: 72000000
Processed lines: 70500000
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Finished processing child process. Exiting..
Processed lines: 71000000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Processed lines: 73000000
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Finished processing child process. Exiting..
Processed lines: 72500000
Finished processing child process. Exiting..
Processed lines: 71000000
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Processed lines: 71500000
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Finished processing child process. Exiting..
Processed lines: 72000000
Processed lines: 72000000
Processed lines: 71500000
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Processed lines: 72000000
Processed lines: 73000000
Finished processing child process. Exiting..
Processed lines: 71500000
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Processed lines: 73000000
Processed lines: 71000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 72500000
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Processed lines: 72000000
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Processed lines: 72000000
Processed lines: 72000000
Processed lines: 71500000
Processed lines: 73000000
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Processed lines: 72500000
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Processed lines: 72500000
Processed lines: 72500000
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Processed lines: 72000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 72500000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 73000000
Processed lines: 73000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 73000000
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28


Processed 73301023 lines in total
Total number of methylation call strings processed: 146602046

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2060013095

Total methylated C's in CpG context:	34898355
Total methylated C's in CHG context:	1383254
Total methylated C's in CHH context:	5644769

Total C to T conversions in CpG context:	232890147
Total C to T conversions in CHG context:	367770942
Total C to T conversions in CHH context:	1417425628

C methylated in CpG context:	13.0%
C methylated in non-CpG context:	0.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias
9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias

Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 136
Maximum read length of Read 2: 136

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: 136
Maximum read length of Read 2: 136

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

CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
Non_CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt Non_CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		9M_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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/071521-cvBS/CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Writing bedGraph to file: 9M_R1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 9M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Sorting input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_context_9M_R1_val_1_bismark_bt2_pe.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Finished BedGraph conversion ...

Found 26 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> 12M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 12M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 12M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 12M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 12M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 12M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 12M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 12M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 13M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 13M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 13M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 13M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 13M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 13M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 13M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 13M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 16F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 16F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 16F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 16F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 16F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 16F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 16F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 16F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 19F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 19F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 19F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 19F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 19F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 19F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 19F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 19F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 22F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 22F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 22F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 22F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 22F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 22F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 22F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 22F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 23M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 23M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 23M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 23M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 23M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 23M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 23M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 23M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 29F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 29F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 29F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 29F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 29F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 29F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 29F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 29F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 31M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 31M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 31M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 31M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 31M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 31M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 31M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 31M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 35F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 35F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 35F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 35F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 35F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 35F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 35F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 35F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 36F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 36F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 36F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 36F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 36F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 36F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 36F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 36F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 39F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 39F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 39F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 39F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 39F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 39F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 39F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 39F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 3F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 3F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 3F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 3F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 3F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 3F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 3F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 3F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 41F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 41F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 41F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 41F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 41F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 41F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 41F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 41F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 44F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 44F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 44F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 44F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 44F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 44F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 44F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 44F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 48M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 48M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 48M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 48M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 48M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 48M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 48M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 48M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 50F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 50F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 50F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 50F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 50F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 50F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 50F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 50F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 52F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 52F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 52F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 52F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 52F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 52F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 52F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 52F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 53F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 53F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 53F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 53F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 53F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 53F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 53F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 53F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 54F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 54F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 54F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 54F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 54F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 54F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 54F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 54F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 59M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 59M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 59M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 59M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 59M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 59M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 59M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 59M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 64M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 64M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 64M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 64M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 64M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 64M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 64M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 64M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 6M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 6M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 6M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 6M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 6M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 6M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 6M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 6M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 76F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 76F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 76F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 76F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 76F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 76F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 76F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 76F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 77F_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 77F_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 77F_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 77F_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 77F_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 77F_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 77F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 77F_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 7M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 7M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 7M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 7M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 7M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 7M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 7M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 7M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================



Writing Bismark HTML report to >> 9M_R1_val_1_bismark_bt2_PE_report.html <<

==============================================================================================================
Using the following alignment report:		> 9M_R1_val_1_bismark_bt2_PE_report.txt <
Processing alignment report 9M_R1_val_1_bismark_bt2_PE_report.txt ...
Complete

Using the following deduplication report:	> 9M_R1_val_1_bismark_bt2_pe.deduplication_report.txt <
Processing deduplication report 9M_R1_val_1_bismark_bt2_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> 9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt <
Processing splitting report 9M_R1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> 9M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt <
Processing M-bias report 9M_R1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


No Bismark/Bowtie2 single-end BAM files detected
Found Bismark/Bowtie2 paired-end files
No Bismark/HISAT2 single-end BAM files detected
No Bismark/HISAT2 paired-end BAM files detected

Generating Bismark summary report from 26 Bismark BAM file(s)...
>> Reading from Bismark report: 12M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 13M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 16F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 19F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 22F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 23M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 29F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 31M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 35F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 36F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 39F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 3F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 41F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 44F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 48M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 50F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 52F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 53F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 54F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 59M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 64M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 6M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 76F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 77F_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 7M_R1_val_1_bismark_bt2_PE_report.txt
>> Reading from Bismark report: 9M_R1_val_1_bismark_bt2_PE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[INFO   ]         multiqc : This is MultiQC v1.8
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching   : /gscratch/scrubbed/sr320/071521-cvBS
[INFO   ]         bismark : Found 26 bismark alignment reports
[INFO   ]         bismark : Found 26 bismark dedup reports
[INFO   ]         bismark : Found 26 bismark methextract reports
[INFO   ]          fastqc : Found 52 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 140 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 140 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
[bam_sort_core] merging from 196 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 112 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
[bam_sort_core] merging from 84 files and 28 in-memory blocks...
Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				12M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 12M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035787.1
Writing cytosine report for chromosome NC_035787.1 (stored 2283366 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2250237 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2021624 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1009987 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3347376 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3096730 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2459811 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2017251 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1716154 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1478817 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 947 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>12M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 12M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				13M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 13M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035780.1
Writing cytosine report for chromosome NC_035780.1 (stored 2267880 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2465296 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1582559 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3345680 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3062465 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2011533 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2016963 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1402020 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1024434 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2312370 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 957 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>13M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 13M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				16F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 16F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035787.1
Writing cytosine report for chromosome NC_035787.1 (stored 2320628 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3111818 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2464396 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2269966 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2018030 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3337005 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1486010 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1000933 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1731853 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2007606 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1342 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>16F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 16F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				19F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 19F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035784.1
Writing cytosine report for chromosome NC_035784.1 (stored 3358514 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2022168 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3086512 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2463550 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2295853 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2019939 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1011381 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1757 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1451946 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2264695 different covered positions)
Writing cytosine report for last chromosome NC_035786.1 (stored 1693138 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>19F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 19F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				22F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 22F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035786.1
Writing cytosine report for chromosome NC_035786.1 (stored 1654942 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2221195 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3270542 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2418823 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 968796 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2930692 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1982334 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1404609 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1621 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1958446 different covered positions)
Writing cytosine report for last chromosome NC_035780.1 (stored 2211220 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>22F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 22F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				23M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 23M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035780.1
Writing cytosine report for chromosome NC_035780.1 (stored 2262295 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3068137 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1712136 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2018067 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3382945 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2034276 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2301547 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2470140 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1482397 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1041473 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 936 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>23M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 23M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				29F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 29F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035784.1
Writing cytosine report for chromosome NC_035784.1 (stored 3318709 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2239860 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3045922 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2281221 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1443303 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2420314 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1990432 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1990712 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1382 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1674522 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 1006870 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>29F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 29F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				31M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 31M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035786.1
Writing cytosine report for chromosome NC_035786.1 (stored 1591087 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2332886 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2903195 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1972932 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3471369 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1936779 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2260712 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1392899 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 938085 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2129790 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 903 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>31M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 31M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				35F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 35F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035785.1
Writing cytosine report for chromosome NC_035785.1 (stored 1426437 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1700145 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2446349 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3340828 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2256165 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3028099 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1007731 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2281384 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2016474 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1996555 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1757 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>35F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 35F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				36F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 36F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035780.1
Writing cytosine report for chromosome NC_035780.1 (stored 2231041 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1709564 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2006036 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2002621 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3056174 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1446714 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2438237 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3313601 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2268610 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1681 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 1028710 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>36F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 36F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				39F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 39F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035786.1
Writing cytosine report for chromosome NC_035786.1 (stored 1665743 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1972719 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2223253 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1006277 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2996548 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3331499 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2231429 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2421543 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1983347 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1431789 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1784 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>39F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 39F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				3F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 3F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035787.1
Writing cytosine report for chromosome NC_035787.1 (stored 2266858 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2398132 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1987641 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1996021 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3365847 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1529082 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2218530 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1690836 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3096603 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1096579 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1630 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>3F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 3F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				41F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 41F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035783.1
Writing cytosine report for chromosome NC_035783.1 (stored 1922861 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2154454 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1372409 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2133796 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1543872 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3228312 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1940753 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2893078 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2320502 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1390 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 936838 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>41F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 41F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				44F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 44F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035784.1
Writing cytosine report for chromosome NC_035784.1 (stored 3521014 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2600554 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1105692 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3295447 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1838961 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2389880 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2132145 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2454438 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1554433 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2117041 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1565 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>44F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 44F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				48M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 48M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035782.1
Writing cytosine report for chromosome NC_035782.1 (stored 2409593 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2987846 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2207955 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1663658 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1970760 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2213204 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1976220 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3271605 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 977735 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1424019 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 996 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>48M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 48M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				50F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 50F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035784.1
Writing cytosine report for chromosome NC_035784.1 (stored 3319024 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2445190 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1028655 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2299695 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2001538 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1724895 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3079333 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1459903 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2248325 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2012085 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1593 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>50F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 50F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				52F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 52F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035782.1
Writing cytosine report for chromosome NC_035782.1 (stored 2465745 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2326505 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2025700 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3375100 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3111708 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2022914 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1024020 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1714239 different covered positions)
Writing cytosine report for chromosome NC_007175.2 (stored 1396 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2283206 different covered positions)
Writing cytosine report for last chromosome NC_035785.1 (stored 1482645 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>52F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 52F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				53F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 53F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035785.1
Writing cytosine report for chromosome NC_035785.1 (stored 1469356 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1697374 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2286229 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3357023 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2266137 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2023298 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2468371 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3087402 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2020729 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1020920 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1668 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>53F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 53F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				54F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 54F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035782.1
Writing cytosine report for chromosome NC_035782.1 (stored 2476787 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3381733 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 2024609 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2263925 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 2023430 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2317586 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1700093 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1476619 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3047017 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1026291 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1501 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>54F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 54F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				59M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 59M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035785.1
Writing cytosine report for chromosome NC_035785.1 (stored 1342825 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2146461 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1913600 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1901658 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3141612 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2834162 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2142337 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2306070 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 910124 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1538012 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 905 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>59M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 59M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				64M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 64M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035782.1
Writing cytosine report for chromosome NC_035782.1 (stored 2408459 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2211476 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1984778 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2224056 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3298882 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1987920 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1005421 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1424250 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2975513 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1677372 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 955 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>64M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 64M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				6M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 6M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035788.1
Writing cytosine report for chromosome NC_035788.1 (stored 2948362 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1938101 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2340704 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2169462 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1930489 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2179033 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3248885 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1380706 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 967419 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1646998 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 990 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>6M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 6M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				76F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 76F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035789.1
Writing cytosine report for chromosome NC_035789.1 (stored 960357 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1988111 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2252044 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2158309 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1978663 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2428062 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3307622 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1675532 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 3003556 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1409504 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1581 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>76F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 76F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				77F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 77F_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035787.1
Writing cytosine report for chromosome NC_035787.1 (stored 2261644 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1997367 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 1011331 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2226752 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1986246 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1435977 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3287286 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2995144 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2417161 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1690288 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 1495 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>77F_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 77F_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				7M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 7M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035782.1
Writing cytosine report for chromosome NC_035782.1 (stored 2415057 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 1421164 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1990315 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3332211 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2950399 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2250806 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 995649 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2221867 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1994301 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1650744 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 980 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>7M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 7M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				9M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/071521-cvBS/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-genome/<
Coverage threshold				0 (all positions will be reported, default)
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: 9M_R1_val_1.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: NC_035785.1
Writing cytosine report for chromosome NC_035785.1 (stored 1376004 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 2934386 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 3323539 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 2169193 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1966949 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 2404901 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 1664000 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 2212185 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 1963993 different covered positions)
Writing cytosine report for chromosome NC_035789.1 (stored 877903 different covered positions)
Writing cytosine report for last chromosome NC_007175.2 (stored 908 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>9M_R1_val_1.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 9M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!