*** Bismark methylation extractor version v0.20.0 ***

Output will be written into the directory: /Volumes/web/metacarcinus/Cvirginica/20181004/
Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark paired-end SAM format specified (default)
Number of cores to be used: 2
Output path specified as: /Volumes/web/metacarcinus/Cvirginica/20181004/


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

Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:	'2G'. Temporary directory used for sorting is the output directory

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bam

skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_10_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_10_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 6098678 lines in total
Total number of methylation call strings processed: 12197356

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	161979006

Total methylated C's in CpG context:	15010256
Total methylated C's in CHG context:	1253545
Total methylated C's in CHH context:	4613320

Total C to T conversions in CpG context:	7412133
Total C to T conversions in CHG context:	34551003
Total C to T conversions in CHH context:	99138749

C methylated in CpG context:	66.9%
C methylated in CHG context:	3.5%
C methylated in CHH context:	4.4%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_1_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_1_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 4407890 lines in total
Total number of methylation call strings processed: 8815780

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	117187042

Total methylated C's in CpG context:	10156041
Total methylated C's in CHG context:	867748
Total methylated C's in CHH context:	3830928

Total C to T conversions in CpG context:	4825412
Total C to T conversions in CHG context:	23903571
Total C to T conversions in CHH context:	73603342

C methylated in CpG context:	67.8%
C methylated in CHG context:	3.5%
C methylated in CHH context:	4.9%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_2_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_2_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 7582898 lines in total
Total number of methylation call strings processed: 15165796

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	190616346

Total methylated C's in CpG context:	16881804
Total methylated C's in CHG context:	1484733
Total methylated C's in CHH context:	7213704

Total C to T conversions in CpG context:	8165931
Total C to T conversions in CHG context:	40637178
Total C to T conversions in CHH context:	116232996

C methylated in CpG context:	67.4%
C methylated in CHG context:	3.5%
C methylated in CHH context:	5.8%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_3_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 8500000
Processed lines: 9000000
Processed lines: 9000000
Processed lines: 9500000
Processed lines: 9500000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_3_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 9734305 lines in total
Total number of methylation call strings processed: 19468610

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	262062166

Total methylated C's in CpG context:	27665110
Total methylated C's in CHG context:	2000329
Total methylated C's in CHH context:	7413378

Total C to T conversions in CpG context:	9692932
Total C to T conversions in CHG context:	56032292
Total C to T conversions in CHH context:	159258125

C methylated in CpG context:	74.1%
C methylated in CHG context:	3.4%
C methylated in CHH context:	4.4%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_4_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_4_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 7423370 lines in total
Total number of methylation call strings processed: 14846740

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	186384892

Total methylated C's in CpG context:	14778915
Total methylated C's in CHG context:	1374799
Total methylated C's in CHH context:	6316301

Total C to T conversions in CpG context:	8756708
Total C to T conversions in CHG context:	38923593
Total C to T conversions in CHH context:	116234576

C methylated in CpG context:	62.8%
C methylated in CHG context:	3.4%
C methylated in CHH context:	5.2%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_5_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 8500000
Processed lines: 9000000
Processed lines: 9000000
Processed lines: 9500000
Processed lines: 9500000
Finished processing child process. Exiting..
Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_5_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 9873285 lines in total
Total number of methylation call strings processed: 19746570

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	252492402

Total methylated C's in CpG context:	20157186
Total methylated C's in CHG context:	1871699
Total methylated C's in CHH context:	7828745

Total C to T conversions in CpG context:	11121885
Total C to T conversions in CHG context:	51406712
Total C to T conversions in CHH context:	160106175

C methylated in CpG context:	64.4%
C methylated in CHG context:	3.5%
C methylated in CHH context:	4.7%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_6_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_6_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 7550283 lines in total
Total number of methylation call strings processed: 15100566

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	190864683

Total methylated C's in CpG context:	17248355
Total methylated C's in CHG context:	1442731
Total methylated C's in CHH context:	6328119

Total C to T conversions in CpG context:	7336625
Total C to T conversions in CHG context:	39733116
Total C to T conversions in CHH context:	118775737

C methylated in CpG context:	70.2%
C methylated in CHG context:	3.5%
C methylated in CHH context:	5.1%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

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

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_7_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 8500000
Processed lines: 9000000
Processed lines: 9000000
Processed lines: 9500000
Processed lines: 9500000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_7_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 9955889 lines in total
Total number of methylation call strings processed: 19911778

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	259380298

Total methylated C's in CpG context:	22460519
Total methylated C's in CHG context:	2034052
Total methylated C's in CHH context:	7897415

Total C to T conversions in CpG context:	10024937
Total C to T conversions in CHG context:	54122929
Total C to T conversions in CHH context:	162840446

C methylated in CpG context:	69.1%
C methylated in CHG context:	3.6%
C methylated in CHH context:	4.6%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_8_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 8500000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_8_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 8727936 lines in total
Total number of methylation call strings processed: 17455872

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	223405198

Total methylated C's in CpG context:	17003347
Total methylated C's in CHG context:	1714400
Total methylated C's in CHH context:	7367274

Total C to T conversions in CpG context:	9662409
Total C to T conversions in CHG context:	46581820
Total C to T conversions in CHH context:	141075948

C methylated in CpG context:	63.8%
C methylated in CHG context:	3.5%
C methylated in CHH context:	5.0%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...

Checking file >>/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 100 --non_directional --genome /gscratch/srlab/strigg/data/Cvirg/Bismark_genome/ -1 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R1.fastq.gz -2 /gscratch/srlab/strigg/data/Cvirg/FASTQS/18-04-07/zr2096_9_s1_R2.fastq.gz -o /gscratch/srlab/strigg/analyses/20181004/"
Processed lines: 500000
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 8500000
Processed lines: 9000000
Processed lines: 9000000
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/Volumes/web/metacarcinus/Cvirginica/20181004/zr2096_9_s1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 9180203 lines in total
Total number of methylation call strings processed: 18360406

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	247569836

Total methylated C's in CpG context:	24620940
Total methylated C's in CHG context:	2094757
Total methylated C's in CHH context:	7736902

Total C to T conversions in CpG context:	9054979
Total C to T conversions in CHG context:	52006634
Total C to T conversions in CHH context:	152055624

C methylated in CpG context:	73.1%
C methylated in CHG context:	3.9%
C methylated in CHH context:	4.8%



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

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 100
Maximum read length of Read 2: 100

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

/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CpG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt /Volumes/web/metacarcinus/Cvirginica/20181004/CHH_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/Volumes/web/metacarcinus/Cvirginica/20181004/<
remove whitespaces:		no
CX context:			no (CpG context only, default)
No-header selected:		no
Sorting method:			Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:		2G
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
Writing bedGraph to file: zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /Volumes/web/metacarcinus/Cvirginica/20181004/
The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
sort: stray character in field spec: invalid field specification `3,3V'
Died at /Users/strigg/anaconda3/bin/bismark2bedGraph line 486.
Finished BedGraph conversion ...