*** Bismark methylation extractor version v0.19.0 ***

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

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

Summarising Bismark methylation extractor parameters:
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Bismark paired-end SAM format specified (default)
Number of cores to be used: 28
Output path specified as: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/


Summarising bedGraph parameters:
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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 >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bam

skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
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skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
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skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_1_S13_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_1_S13_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 21575802 lines in total
Total number of methylation call strings processed: 43151604

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	525743553

Total methylated C's in CpG context:	38491726
Total methylated C's in CHG context:	1620612
Total methylated C's in CHH context:	7995683

Total C to T conversions in CpG context:	12727165
Total C to T conversions in CHG context:	130379612
Total C to T conversions in CHH context:	334528755

C methylated in CpG context:	75.2%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.3%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_26psu_1_S13_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_2_S14_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_2_S14_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bam

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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17189294 lines in total
Total number of methylation call strings processed: 34378588

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	424581801

Total methylated C's in CpG context:	30556058
Total methylated C's in CHG context:	1286286
Total methylated C's in CHH context:	7231607

Total C to T conversions in CpG context:	9584179
Total C to T conversions in CHG context:	105180345
Total C to T conversions in CHH context:	270743326

C methylated in CpG context:	76.1%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_26psu_2_S14_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bam

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skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_027300.1	LN:159038749
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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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_3_S15_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_3_S15_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14795488 lines in total
Total number of methylation call strings processed: 29590976

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	363083584

Total methylated C's in CpG context:	23797835
Total methylated C's in CHG context:	1137390
Total methylated C's in CHH context:	11762442

Total C to T conversions in CpG context:	7321578
Total C to T conversions in CHG context:	92991548
Total C to T conversions in CHH context:	226072791

C methylated in CpG context:	76.5%
C methylated in CHG context:	1.2%
C methylated in CHH context:	4.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_26psu_3_S15_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
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skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
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skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
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skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
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skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_4_S16_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_26psu_4_S16_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17134770 lines in total
Total number of methylation call strings processed: 34269540

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	399516006

Total methylated C's in CpG context:	29302931
Total methylated C's in CHG context:	1193831
Total methylated C's in CHH context:	7502553

Total C to T conversions in CpG context:	9119754
Total C to T conversions in CHG context:	99930693
Total C to T conversions in CHH context:	252466244

C methylated in CpG context:	76.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_26psu_4_S16_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
skipping SAM header line:	@SQ	SN:NC_027303.1	LN:82398023
skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
skipping SAM header line:	@SQ	SN:NC_027312.1	LN:107758822
skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
skipping SAM header line:	@SQ	SN:NC_027314.1	LN:103963436
skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_1_S1_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_1_S1_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
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Finished processing child process. Exiting..
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 19691590 lines in total
Total number of methylation call strings processed: 39383180

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	436346960

Total methylated C's in CpG context:	33075407
Total methylated C's in CHG context:	1411341
Total methylated C's in CHH context:	7298653

Total C to T conversions in CpG context:	10400209
Total C to T conversions in CHG context:	108343537
Total C to T conversions in CHH context:	275817813

C methylated in CpG context:	76.1%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_32psu_1_S1_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_2_S2_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_2_S2_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Now waiting for all child processes to complete
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Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 19214925 lines in total
Total number of methylation call strings processed: 38429850

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	427266557

Total methylated C's in CpG context:	30881725
Total methylated C's in CHG context:	1415576
Total methylated C's in CHH context:	8558961

Total C to T conversions in CpG context:	10195572
Total C to T conversions in CHG context:	106925740
Total C to T conversions in CHH context:	269288983

C methylated in CpG context:	75.2%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.1%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_32psu_2_S2_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_3_S3_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_3_S3_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14295142 lines in total
Total number of methylation call strings processed: 28590284

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	307080014

Total methylated C's in CpG context:	22748845
Total methylated C's in CHG context:	1035467
Total methylated C's in CHH context:	5950984

Total C to T conversions in CpG context:	7297930
Total C to T conversions in CHG context:	78100524
Total C to T conversions in CHH context:	191946264

C methylated in CpG context:	75.7%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.0%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_32psu_3_S3_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
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skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
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skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
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skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
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skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
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skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_4_S4_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/16C_32psu_4_S4_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 15610579 lines in total
Total number of methylation call strings processed: 31221158

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	427716510

Total methylated C's in CpG context:	28525816
Total methylated C's in CHG context:	1214209
Total methylated C's in CHH context:	5858980

Total C to T conversions in CpG context:	9286354
Total C to T conversions in CHG context:	102161791
Total C to T conversions in CHH context:	280669360

C methylated in CpG context:	75.4%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.0%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 16C_32psu_4_S4_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
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skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_1_S9_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_1_S9_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bam

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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17929187 lines in total
Total number of methylation call strings processed: 35858374

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	444712492

Total methylated C's in CpG context:	31989352
Total methylated C's in CHG context:	1453612
Total methylated C's in CHH context:	7425008

Total C to T conversions in CpG context:	10092222
Total C to T conversions in CHG context:	110730651
Total C to T conversions in CHH context:	283021647

C methylated in CpG context:	76.0%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_26psu_1_S9_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
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skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
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skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_2_S10_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_2_S10_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 19498562 lines in total
Total number of methylation call strings processed: 38997124

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	463843415

Total methylated C's in CpG context:	33508800
Total methylated C's in CHG context:	1373618
Total methylated C's in CHH context:	6818446

Total C to T conversions in CpG context:	10758076
Total C to T conversions in CHG context:	115361183
Total C to T conversions in CHH context:	296023292

C methylated in CpG context:	75.7%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.3%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_26psu_2_S10_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
skipping SAM header line:	@SQ	SN:NC_027303.1	LN:82398023
skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
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skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
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skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
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skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_3_S11_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_3_S11_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17826813 lines in total
Total number of methylation call strings processed: 35653626

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	372124371

Total methylated C's in CpG context:	30097740
Total methylated C's in CHG context:	1279302
Total methylated C's in CHH context:	6710531

Total C to T conversions in CpG context:	9223028
Total C to T conversions in CHG context:	95755436
Total C to T conversions in CHH context:	229058334

C methylated in CpG context:	76.5%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.8%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_26psu_3_S11_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
skipping SAM header line:	@SQ	SN:NC_027303.1	LN:82398023
skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
skipping SAM header line:	@SQ	SN:NC_027312.1	LN:107758822
skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
skipping SAM header line:	@SQ	SN:NC_027314.1	LN:103963436
skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_4_S12_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_26psu_4_S12_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 12778751 lines in total
Total number of methylation call strings processed: 25557502

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	355589329

Total methylated C's in CpG context:	19888926
Total methylated C's in CHG context:	1058278
Total methylated C's in CHH context:	8266584

Total C to T conversions in CpG context:	6629898
Total C to T conversions in CHG context:	87993150
Total C to T conversions in CHH context:	231752493

C methylated in CpG context:	75.0%
C methylated in CHG context:	1.2%
C methylated in CHH context:	3.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_26psu_4_S12_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
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skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
skipping SAM header line:	@SQ	SN:NC_027312.1	LN:107758822
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skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_1_S5_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_1_S5_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14328928 lines in total
Total number of methylation call strings processed: 28657856

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	278314219

Total methylated C's in CpG context:	23331520
Total methylated C's in CHG context:	959495
Total methylated C's in CHH context:	5171031

Total C to T conversions in CpG context:	7470640
Total C to T conversions in CHG context:	72314798
Total C to T conversions in CHH context:	169066735

C methylated in CpG context:	75.7%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.0%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_32psu_1_S5_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam
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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bam

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skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_027300.1	LN:159038749
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skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_2_S6_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_2_S6_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 12952118 lines in total
Total number of methylation call strings processed: 25904236

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	304262698

Total methylated C's in CpG context:	22620248
Total methylated C's in CHG context:	904544
Total methylated C's in CHH context:	4710546

Total C to T conversions in CpG context:	7467578
Total C to T conversions in CHG context:	75902050
Total C to T conversions in CHH context:	192657732

C methylated in CpG context:	75.2%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_32psu_2_S6_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_3_S7_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_3_S7_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14341620 lines in total
Total number of methylation call strings processed: 28683240

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	317667947

Total methylated C's in CpG context:	23852160
Total methylated C's in CHG context:	963524
Total methylated C's in CHH context:	5361075

Total C to T conversions in CpG context:	7935237
Total C to T conversions in CHG context:	79976201
Total C to T conversions in CHH context:	199579750

C methylated in CpG context:	75.0%
C methylated in CHG context:	1.2%
C methylated in CHH context:	2.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_32psu_3_S7_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bam

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skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_027300.1	LN:159038749
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_4_S8_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/8C_32psu_4_S8_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14301040 lines in total
Total number of methylation call strings processed: 28602080

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	374621407

Total methylated C's in CpG context:	26375521
Total methylated C's in CHG context:	1134015
Total methylated C's in CHH context:	4745652

Total C to T conversions in CpG context:	9182060
Total C to T conversions in CHG context:	89515972
Total C to T conversions in CHH context:	243668187

C methylated in CpG context:	74.2%
C methylated in CHG context:	1.3%
C methylated in CHH context:	1.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: 8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file 8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file 8C_32psu_4_S8_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
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skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_1_S19_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_1_S19_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17450311 lines in total
Total number of methylation call strings processed: 34900622

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	419186365

Total methylated C's in CpG context:	32557805
Total methylated C's in CHG context:	1334418
Total methylated C's in CHH context:	6208970

Total C to T conversions in CpG context:	9930072
Total C to T conversions in CHG context:	103485390
Total C to T conversions in CHH context:	265669710

C methylated in CpG context:	76.6%
C methylated in CHG context:	1.3%
C methylated in CHH context:	2.3%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file CTRL_16C_26psu_1_S19_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
skipping SAM header line:	@SQ	SN:NC_027303.1	LN:82398023
skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
skipping SAM header line:	@SQ	SN:NC_027312.1	LN:107758822
skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
skipping SAM header line:	@SQ	SN:NC_027314.1	LN:103963436
skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_16C_26psu_2_S21_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 12858052 lines in total
Total number of methylation call strings processed: 25716104

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	268615619

Total methylated C's in CpG context:	23480289
Total methylated C's in CHG context:	1199325
Total methylated C's in CHH context:	4807728

Total C to T conversions in CpG context:	6987557
Total C to T conversions in CHG context:	68886678
Total C to T conversions in CHH context:	163254042

C methylated in CpG context:	77.1%
C methylated in CHG context:	1.7%
C methylated in CHH context:	2.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file CTRL_16C_26psu_2_S21_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
skipping SAM header line:	@SQ	SN:NC_027301.1	LN:72943711
skipping SAM header line:	@SQ	SN:NC_027302.1	LN:92503428
skipping SAM header line:	@SQ	SN:NC_027303.1	LN:82398023
skipping SAM header line:	@SQ	SN:NC_027304.1	LN:80503876
skipping SAM header line:	@SQ	SN:NC_027305.1	LN:87043187
skipping SAM header line:	@SQ	SN:NC_027306.1	LN:58785265
skipping SAM header line:	@SQ	SN:NC_027307.1	LN:26434011
skipping SAM header line:	@SQ	SN:NC_027308.1	LN:141712163
skipping SAM header line:	@SQ	SN:NC_027309.1	LN:116138521
skipping SAM header line:	@SQ	SN:NC_027310.1	LN:93888508
skipping SAM header line:	@SQ	SN:NC_027311.1	LN:91880962
skipping SAM header line:	@SQ	SN:NC_027312.1	LN:107758822
skipping SAM header line:	@SQ	SN:NC_027313.1	LN:93901823
skipping SAM header line:	@SQ	SN:NC_027314.1	LN:103963436
skipping SAM header line:	@SQ	SN:NC_027315.1	LN:87796322
skipping SAM header line:	@SQ	SN:NC_027316.1	LN:57682537
skipping SAM header line:	@SQ	SN:NC_027317.1	LN:70695409
skipping SAM header line:	@SQ	SN:NC_027318.1	LN:82978132
skipping SAM header line:	@SQ	SN:NC_027319.1	LN:86795997
skipping SAM header line:	@SQ	SN:NC_027320.1	LN:58021487
skipping SAM header line:	@SQ	SN:NC_027321.1	LN:63420196
skipping SAM header line:	@SQ	SN:NC_027322.1	LN:49854004
skipping SAM header line:	@SQ	SN:NC_027323.1	LN:48650976
skipping SAM header line:	@SQ	SN:NC_027324.1	LN:51481326
skipping SAM header line:	@SQ	SN:NC_027325.1	LN:47900953
skipping SAM header line:	@SQ	SN:NC_027326.1	LN:43943985
skipping SAM header line:	@SQ	SN:NC_027327.1	LN:39600944
skipping SAM header line:	@SQ	SN:NC_027328.1	LN:42488238
skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_1_S17_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_1_S17_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 14375724 lines in total
Total number of methylation call strings processed: 28751448

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	359140236

Total methylated C's in CpG context:	23980460
Total methylated C's in CHG context:	955543
Total methylated C's in CHH context:	4665204

Total C to T conversions in CpG context:	7603829
Total C to T conversions in CHG context:	84912469
Total C to T conversions in CHH context:	237022731

C methylated in CpG context:	75.9%
C methylated in CHG context:	1.1%
C methylated in CHH context:	1.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file CTRL_8C_26psu_1_S17_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.
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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.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_027300.1	LN:159038749
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skipping SAM header line:	@SQ	SN:NC_001960.1	LN:16665
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,-0.6 -p 4 --non_directional --dovetail --genome /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_2_S18_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/CTRL_8C_26psu_2_S18_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190828_Salmo"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe_splitting_report.txt'
Merging from these individual files:

Processed 17301715 lines in total
Total number of methylation call strings processed: 34603430

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	329200773

Total methylated C's in CpG context:	28092889
Total methylated C's in CHG context:	1131167
Total methylated C's in CHH context:	7721750

Total C to T conversions in CpG context:	8311760
Total C to T conversions in CHG context:	85385686
Total C to T conversions in CHH context:	198557521

C methylated in CpG context:	77.2%
C methylated in CHG context:	1.3%
C methylated in CHH context:	3.7%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
Determining maximum read lengths for M-Bias plots
Maximum read length of Read 1: 145
Maximum read length of Read 2: 145

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: 145
Maximum read length of Read 2: 145

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

/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CpG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CHH_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190828_Salmo/<
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: CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190828_Salmo/
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 CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Finished writing methylation calls from CpG_OB_CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.txt to merged temp file
Sorting input file CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file CTRL_8C_26psu_2_S18_R1_001_val_1_bismark_bt2_pe.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...