*** 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/20190814_Calig/


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/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:Cr_scaffold0000001	LN:36897007
skipping SAM header line:	@SQ	SN:Cr_scaffold0000002	LN:35124817
skipping SAM header line:	@SQ	SN:Cr_scaffold0000003	LN:33138466
skipping SAM header line:	@SQ	SN:Cr_scaffold0000004	LN:31456035
skipping SAM header line:	@SQ	SN:Cr_scaffold0000005	LN:30612693
skipping SAM header line:	@SQ	SN:Cr_scaffold0000006	LN:30259679
skipping SAM header line:	@SQ	SN:Cr_scaffold0000007	LN:29872177
skipping SAM header line:	@SQ	SN:Cr_scaffold0000008	LN:27803016
skipping SAM header line:	@SQ	SN:Cr_scaffold0000009	LN:25126635
skipping SAM header line:	@SQ	SN:Cr_scaffold0000010	LN:24815513
skipping SAM header line:	@SQ	SN:Cr_scaffold0000011	LN:35794548
skipping SAM header line:	@SQ	SN:Cr_scaffold0000012	LN:22957860
skipping SAM header line:	@SQ	SN:Cr_scaffold0000013	LN:21502856
skipping SAM header line:	@SQ	SN:Cr_scaffold0000014	LN:21148584
skipping SAM header line:	@SQ	SN:Cr_scaffold0000015	LN:19091682
skipping SAM header line:	@SQ	SN:Cr_scaffold0000016	LN:18525937
skipping SAM header line:	@SQ	SN:Cr_scaffold0000017	LN:17562062
skipping SAM header line:	@SQ	SN:Cr_scaffold0000018	LN:14680182
skipping SAM header line:	@SQ	SN:Cr_scaffold0000019	LN:14290452
skipping SAM header line:	@SQ	SN:Cr_scaffold0000020	LN:8286978
skipping SAM header line:	@SQ	SN:Cr_scaffold0000021	LN:8023048
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/Caligus/GENOMES -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F1_S20_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F1_S20_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190814_Calig"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 39805619 lines in total
Total number of methylation call strings processed: 79611238

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1080632321

Total methylated C's in CpG context:	2147644
Total methylated C's in CHG context:	2047093
Total methylated C's in CHH context:	11328501

Total C to T conversions in CpG context:	160702911
Total C to T conversions in CHG context:	167901509
Total C to T conversions in CHH context:	736504663

C methylated in CpG context:	1.3%
C methylated in CHG context:	1.2%
C methylated in CHH context:	1.5%



Merging individual M-bias reports into overall M-bias statistics from these 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/20190814_Calig/CpG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190814_Calig/<
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: Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190814_Calig/
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 Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...

...passed!
Writing result file containing methylation information for C in CpG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:Cr_scaffold0000001	LN:36897007
skipping SAM header line:	@SQ	SN:Cr_scaffold0000002	LN:35124817
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skipping SAM header line:	@SQ	SN:Cr_scaffold0000010	LN:24815513
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skipping SAM header line:	@SQ	SN:Cr_scaffold0000020	LN:8286978
skipping SAM header line:	@SQ	SN:Cr_scaffold0000021	LN:8023048
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/Caligus/GENOMES -1 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F2_S22_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/TRIMG_adapt_5bp/TRIM_cat/Sealice_F2_S22_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190814_Calig"
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 26624180 lines in total
Total number of methylation call strings processed: 53248360

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	689054985

Total methylated C's in CpG context:	1326595
Total methylated C's in CHG context:	1172949
Total methylated C's in CHH context:	7270421

Total C to T conversions in CpG context:	109026006
Total C to T conversions in CHG context:	112949809
Total C to T conversions in CHH context:	457309205

C methylated in CpG context:	1.2%
C methylated in CHG context:	1.0%
C methylated in CHH context:	1.6%



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/20190814_Calig/CpG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CpG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190814_Calig/CHH_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190814_Calig/<
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: Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190814_Calig/
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 Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...