*** Bismark methylation extractor version v0.25.1 ***

Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/
Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 8
First 10 bp will be disregarded when processing the methylation call string
Last 2 bp will be disregarded when processing the methylation call string
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 path specified as: /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/


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:	'20G'. Temporary directory used for sorting is the output directory

Checking file >>../data/methylation/dedup/SRR6995995.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context to /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/CpG_context_SRR6995995.txt.gz
Writing result file containing methylation information for C in any other context to /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/Non_CpG_context_SRR6995995.txt.gz

Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam


Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam


Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam


Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam


Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam


Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam

Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.bam

Now reading in Bismark result file ../data/methylation/dedup/SRR6995995.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:v0.25.1	CL:"bismark --genome ../data/genome/bismark --non_directional --score_min L,0,-0.6 --parallel 6 --output_dir ../data/bismark --temp_dir ../data/bismark ../data/trimmed-reads/SRR6995995_trimmed.fq.gz"
skipping SAM header line:	@PG	ID:samtools	PN:samtools	PP:Bismark	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bSh -
skipping SAM header line:	@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/bismark/SRR6995995_trimmed.fq.gz.temp.1_bismark_bt2.bam
skipping SAM header line:	@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view --threads 4 -bSh -
skipping SAM header line:	@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.22.1	CL:samtools view -h ../data/bismark/SRR6995995.bam
skipping SAM header line:	@PG	ID:samtools.4	PN:samtools	PP:samtools.3	VN:1.22.1	CL:samtools view -bS -
skipping SAM header line:	@PG	ID:samtools.5	PN:samtools	PP:samtools.4	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h --threads 1 ../data/bismark/SRR6995995.nonCG_filtered.bam
skipping SAM header line:	@PG	ID:samtools.6	PN:samtools	PP:samtools.5	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bS --threads 1 -
skipping SAM header line:	@PG	ID:samtools.7	PN:samtools	PP:samtools.6	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h ../data/methylation/dedup/SRR6995995.bam
Processed lines: 500000
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Finished processing child process. Exiting..
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Now waiting for all child processes to complete
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All child process successfully finished.
Merging individual splitting reports into overall report: '/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt'
Merging from these individual files:
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.1
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.2
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.3
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.4
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.5
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.6
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.7
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.8


Processed 4435166 lines in total
Total number of methylation call strings processed: 4435166

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	73137008

Total methylated C's in CpG context:	8288247
Total methylated C's in CHG context:	276645
Total methylated C's in CHH context:	474611

Total C to T conversions in CpG context:	7415115
Total C to T conversions in CHG context:	19248592
Total C to T conversions in CHH context:	37433798

C methylated in CpG context:	52.8%
C methylated in non-CpG context:	1.3%



Merging individual M-bias reports into overall M-bias statistics from these 8 individual files:
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.1.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.2.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.3.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.4.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.5.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.6.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.7.mbias
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/SRR6995995_splitting_report.txt.8.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 89

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 89

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

/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/CpG_context_SRR6995995.txt.gz contains data ->	kept

gzip: stdout: Broken pipe
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/Non_CpG_context_SRR6995995.txt.gz contains data ->	kept


Using these input files: /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/CpG_context_SRR6995995.txt.gz /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/Non_CpG_context_SRR6995995.txt.gz

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		SRR6995995.bedGraph.gz
output directory:		>/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/<
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:		20G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/CpG_context_SRR6995995.txt.gz

Writing bedGraph to file: SRR6995995.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: SRR6995995.bismark.cov.gz

Changed directory to /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/methylation/dedup/
Now writing methylation information for file >>CpG_context_SRR6995995.txt.gz<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_context_SRR6995995.txt.gz

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_context_SRR6995995.txt.gz.chrNC_035784.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035780.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035786.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035782.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035783.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035788.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035789.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035785.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035787.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_035781.1.methXtractor.temp
CpG_context_SRR6995995.txt.gz.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_007175.2.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035780.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035781.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035782.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035783.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035784.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035785.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035786.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035787.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035788.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_context_SRR6995995.txt.gz.chrNC_035789.1.methXtractor.temp by positions (using -S of 20G)
Successfully deleted the temporary input file CpG_context_SRR6995995.txt.gz.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...


gzip: stdout: Broken pipe