*** 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:
===============================================================
Bismark paired-end SAM format specified (default)
Number of cores to be used: 28
Output path specified as: /gscratch/scrubbed/strigg/analyses/20190806_v074/


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

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

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_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/20190806_v074/CpG_OT_EPI-205_S26_L004_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/20190806_v074/CpG_CTOT_EPI-205_S26_L004_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/20190806_v074/CpG_CTOB_EPI-205_S26_L004_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/20190806_v074/CpG_OB_EPI-205_S26_L004_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/20190806_v074/CHG_OT_EPI-205_S26_L004_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/20190806_v074/CHG_CTOT_EPI-205_S26_L004_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/20190806_v074/CHG_CTOB_EPI-205_S26_L004_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/20190806_v074/CHG_OB_EPI-205_S26_L004_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/20190806_v074/CHH_OT_EPI-205_S26_L004_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/20190806_v074/CHH_CTOT_EPI-205_S26_L004_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/20190806_v074/CHH_CTOB_EPI-205_S26_L004_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/20190806_v074/CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_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:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
skipping SAM header line:	@SQ	SN:PGA_scaffold3__111_contigs__length_57743597	LN:57743597
skipping SAM header line:	@SQ	SN:PGA_scaffold4__129_contigs__length_65288255	LN:65288255
skipping SAM header line:	@SQ	SN:PGA_scaffold5__109_contigs__length_67248332	LN:67248332
skipping SAM header line:	@SQ	SN:PGA_scaffold6__104_contigs__length_61759565	LN:61759565
skipping SAM header line:	@SQ	SN:PGA_scaffold7__69_contigs__length_43120122	LN:43120122
skipping SAM header line:	@SQ	SN:PGA_scaffold8__63_contigs__length_61151155	LN:61151155
skipping SAM header line:	@SQ	SN:PGA_scaffold9__45_contigs__length_38581958	LN:38581958
skipping SAM header line:	@SQ	SN:PGA_scaffold10__49_contigs__length_53961475	LN:53961475
skipping SAM header line:	@SQ	SN:PGA_scaffold11__79_contigs__length_51449921	LN:51449921
skipping SAM header line:	@SQ	SN:PGA_scaffold12__71_contigs__length_50438331	LN:50438331
skipping SAM header line:	@SQ	SN:PGA_scaffold13__52_contigs__length_44396874	LN:44396874
skipping SAM header line:	@SQ	SN:PGA_scaffold14__91_contigs__length_45393038	LN:45393038
skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
skipping SAM header line:	@SQ	SN:PGA_scaffold16__33_contigs__length_31980953	LN:31980953
skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-205_S26_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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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/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5150110 lines in total
Total number of methylation call strings processed: 10300220

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	103331667

Total methylated C's in CpG context:	4086624
Total methylated C's in CHG context:	624807
Total methylated C's in CHH context:	2760965

Total C to T conversions in CpG context:	10383710
Total C to T conversions in CHG context:	21368446
Total C to T conversions in CHH context:	64107115

C methylated in CpG context:	28.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	4.1%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-205_S26_L004_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 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_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/20190806_v074/CpG_OT_EPI-206_S27_L004_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/20190806_v074/CpG_CTOT_EPI-206_S27_L004_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/20190806_v074/CpG_CTOB_EPI-206_S27_L004_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/20190806_v074/CpG_OB_EPI-206_S27_L004_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/20190806_v074/CHG_OT_EPI-206_S27_L004_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/20190806_v074/CHG_CTOT_EPI-206_S27_L004_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/20190806_v074/CHG_CTOB_EPI-206_S27_L004_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/20190806_v074/CHG_OB_EPI-206_S27_L004_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/20190806_v074/CHH_OT_EPI-206_S27_L004_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/20190806_v074/CHH_CTOT_EPI-206_S27_L004_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/20190806_v074/CHH_CTOB_EPI-206_S27_L004_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/20190806_v074/CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_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/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
skipping SAM header line:	@SQ	SN:PGA_scaffold3__111_contigs__length_57743597	LN:57743597
skipping SAM header line:	@SQ	SN:PGA_scaffold4__129_contigs__length_65288255	LN:65288255
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skipping SAM header line:	@SQ	SN:PGA_scaffold12__71_contigs__length_50438331	LN:50438331
skipping SAM header line:	@SQ	SN:PGA_scaffold13__52_contigs__length_44396874	LN:44396874
skipping SAM header line:	@SQ	SN:PGA_scaffold14__91_contigs__length_45393038	LN:45393038
skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
skipping SAM header line:	@SQ	SN:PGA_scaffold16__33_contigs__length_31980953	LN:31980953
skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-206_S27_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 7495147 lines in total
Total number of methylation call strings processed: 14990294

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	155778901

Total methylated C's in CpG context:	6079013
Total methylated C's in CHG context:	928079
Total methylated C's in CHH context:	4316185

Total C to T conversions in CpG context:	15472822
Total C to T conversions in CHG context:	32432818
Total C to T conversions in CHH context:	96549984

C methylated in CpG context:	28.2%
C methylated in CHG context:	2.8%
C methylated in CHH context:	4.3%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-206_S27_L004_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 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_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/20190806_v074/CpG_OT_EPI-214_S30_L004_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/20190806_v074/CpG_CTOT_EPI-214_S30_L004_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/20190806_v074/CpG_CTOB_EPI-214_S30_L004_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/20190806_v074/CpG_OB_EPI-214_S30_L004_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/20190806_v074/CHG_OT_EPI-214_S30_L004_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/20190806_v074/CHG_CTOT_EPI-214_S30_L004_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/20190806_v074/CHG_CTOB_EPI-214_S30_L004_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/20190806_v074/CHG_OB_EPI-214_S30_L004_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/20190806_v074/CHH_OT_EPI-214_S30_L004_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/20190806_v074/CHH_CTOT_EPI-214_S30_L004_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/20190806_v074/CHH_CTOB_EPI-214_S30_L004_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/20190806_v074/CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_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/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
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skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-214_S30_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 10132897 lines in total
Total number of methylation call strings processed: 20265794

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	219999425

Total methylated C's in CpG context:	7962551
Total methylated C's in CHG context:	1195467
Total methylated C's in CHH context:	5188264

Total C to T conversions in CpG context:	22256008
Total C to T conversions in CHG context:	45016568
Total C to T conversions in CHH context:	138380567

C methylated in CpG context:	26.3%
C methylated in CHG context:	2.6%
C methylated in CHH context:	3.6%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-214_S30_L004_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 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_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/20190806_v074/CpG_OT_EPI-215_S31_L004_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/20190806_v074/CpG_CTOT_EPI-215_S31_L004_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/20190806_v074/CpG_CTOB_EPI-215_S31_L004_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/20190806_v074/CpG_OB_EPI-215_S31_L004_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/20190806_v074/CHG_OT_EPI-215_S31_L004_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/20190806_v074/CHG_CTOT_EPI-215_S31_L004_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/20190806_v074/CHG_CTOB_EPI-215_S31_L004_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/20190806_v074/CHG_OB_EPI-215_S31_L004_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/20190806_v074/CHH_OT_EPI-215_S31_L004_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/20190806_v074/CHH_CTOT_EPI-215_S31_L004_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/20190806_v074/CHH_CTOB_EPI-215_S31_L004_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/20190806_v074/CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_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/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.

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Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
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skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-215_S31_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 7206776 lines in total
Total number of methylation call strings processed: 14413552

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	153126104

Total methylated C's in CpG context:	6350237
Total methylated C's in CHG context:	939969
Total methylated C's in CHH context:	4316105

Total C to T conversions in CpG context:	14417738
Total C to T conversions in CHG context:	31452326
Total C to T conversions in CHH context:	95649729

C methylated in CpG context:	30.6%
C methylated in CHG context:	2.9%
C methylated in CHH context:	4.3%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-215_S31_L004_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 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_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/20190806_v074/CpG_OT_EPI-220_S32_L004_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/20190806_v074/CpG_CTOT_EPI-220_S32_L004_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/20190806_v074/CpG_CTOB_EPI-220_S32_L004_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/20190806_v074/CpG_OB_EPI-220_S32_L004_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/20190806_v074/CHG_OT_EPI-220_S32_L004_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/20190806_v074/CHG_CTOT_EPI-220_S32_L004_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/20190806_v074/CHG_CTOB_EPI-220_S32_L004_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/20190806_v074/CHG_OB_EPI-220_S32_L004_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/20190806_v074/CHH_OT_EPI-220_S32_L004_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/20190806_v074/CHH_CTOT_EPI-220_S32_L004_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/20190806_v074/CHH_CTOB_EPI-220_S32_L004_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/20190806_v074/CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_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/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
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skipping SAM header line:	@SQ	SN:PGA_scaffold9__45_contigs__length_38581958	LN:38581958
skipping SAM header line:	@SQ	SN:PGA_scaffold10__49_contigs__length_53961475	LN:53961475
skipping SAM header line:	@SQ	SN:PGA_scaffold11__79_contigs__length_51449921	LN:51449921
skipping SAM header line:	@SQ	SN:PGA_scaffold12__71_contigs__length_50438331	LN:50438331
skipping SAM header line:	@SQ	SN:PGA_scaffold13__52_contigs__length_44396874	LN:44396874
skipping SAM header line:	@SQ	SN:PGA_scaffold14__91_contigs__length_45393038	LN:45393038
skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
skipping SAM header line:	@SQ	SN:PGA_scaffold16__33_contigs__length_31980953	LN:31980953
skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-220_S32_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5203101 lines in total
Total number of methylation call strings processed: 10406202

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	113239580

Total methylated C's in CpG context:	4266656
Total methylated C's in CHG context:	745451
Total methylated C's in CHH context:	5486351

Total C to T conversions in CpG context:	10689611
Total C to T conversions in CHG context:	22638518
Total C to T conversions in CHH context:	69412993

C methylated in CpG context:	28.5%
C methylated in CHG context:	3.2%
C methylated in CHH context:	7.3%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-220_S32_L004_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 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_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/20190806_v074/CpG_OT_EPI-221_S33_L004_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/20190806_v074/CpG_CTOT_EPI-221_S33_L004_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/20190806_v074/CpG_CTOB_EPI-221_S33_L004_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/20190806_v074/CpG_OB_EPI-221_S33_L004_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/20190806_v074/CHG_OT_EPI-221_S33_L004_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/20190806_v074/CHG_CTOT_EPI-221_S33_L004_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/20190806_v074/CHG_CTOB_EPI-221_S33_L004_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/20190806_v074/CHG_OB_EPI-221_S33_L004_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/20190806_v074/CHH_OT_EPI-221_S33_L004_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/20190806_v074/CHH_CTOT_EPI-221_S33_L004_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/20190806_v074/CHH_CTOB_EPI-221_S33_L004_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/20190806_v074/CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_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/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
skipping SAM header line:	@SQ	SN:PGA_scaffold3__111_contigs__length_57743597	LN:57743597
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skipping SAM header line:	@SQ	SN:PGA_scaffold12__71_contigs__length_50438331	LN:50438331
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skipping SAM header line:	@SQ	SN:PGA_scaffold14__91_contigs__length_45393038	LN:45393038
skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
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skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-221_S33_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Finished processing child process. Exiting..
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 5583786 lines in total
Total number of methylation call strings processed: 11167572

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	119677841

Total methylated C's in CpG context:	4584474
Total methylated C's in CHG context:	781930
Total methylated C's in CHH context:	5079039

Total C to T conversions in CpG context:	11342306
Total C to T conversions in CHG context:	24097448
Total C to T conversions in CHH context:	73792644

C methylated in CpG context:	28.8%
C methylated in CHG context:	3.1%
C methylated in CHH context:	6.4%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-221_S33_L004_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 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_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/20190806_v074/CpG_OT_EPI-226_S34_L004_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/20190806_v074/CpG_CTOT_EPI-226_S34_L004_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/20190806_v074/CpG_CTOB_EPI-226_S34_L004_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/20190806_v074/CpG_OB_EPI-226_S34_L004_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/20190806_v074/CHG_OT_EPI-226_S34_L004_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/20190806_v074/CHG_CTOT_EPI-226_S34_L004_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/20190806_v074/CHG_CTOB_EPI-226_S34_L004_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/20190806_v074/CHG_OB_EPI-226_S34_L004_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/20190806_v074/CHH_OT_EPI-226_S34_L004_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/20190806_v074/CHH_CTOT_EPI-226_S34_L004_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/20190806_v074/CHH_CTOB_EPI-226_S34_L004_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/20190806_v074/CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_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/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
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skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
skipping SAM header line:	@SQ	SN:PGA_scaffold16__33_contigs__length_31980953	LN:31980953
skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-226_S34_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Processed lines: 4000000
Processed lines: 4000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Processed lines: 4000000
Processed lines: 4000000
Processed lines: 4000000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..

Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 4194258 lines in total
Total number of methylation call strings processed: 8388516

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	93695995

Total methylated C's in CpG context:	3724305
Total methylated C's in CHG context:	621189
Total methylated C's in CHH context:	4477609

Total C to T conversions in CpG context:	8646879
Total C to T conversions in CHG context:	18759074
Total C to T conversions in CHH context:	57466939

C methylated in CpG context:	30.1%
C methylated in CHG context:	3.2%
C methylated in CHH context:	7.2%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-226_S34_L004_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 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_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/20190806_v074/CpG_OT_EPI-227_S35_L004_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/20190806_v074/CpG_CTOT_EPI-227_S35_L004_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/20190806_v074/CpG_CTOB_EPI-227_S35_L004_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/20190806_v074/CpG_OB_EPI-227_S35_L004_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/20190806_v074/CHG_OT_EPI-227_S35_L004_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/20190806_v074/CHG_CTOT_EPI-227_S35_L004_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/20190806_v074/CHG_CTOB_EPI-227_S35_L004_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/20190806_v074/CHG_OB_EPI-227_S35_L004_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/20190806_v074/CHH_OT_EPI-227_S35_L004_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/20190806_v074/CHH_CTOT_EPI-227_S35_L004_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/20190806_v074/CHH_CTOB_EPI-227_S35_L004_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/20190806_v074/CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

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

Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_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/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Now reading in Bismark result file /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam

Warning: unable to close filehandle IN properly.
Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:PGA_scaffold1__77_contigs__length_89643857	LN:89643857
skipping SAM header line:	@SQ	SN:PGA_scaffold2__36_contigs__length_69596280	LN:69596280
skipping SAM header line:	@SQ	SN:PGA_scaffold3__111_contigs__length_57743597	LN:57743597
skipping SAM header line:	@SQ	SN:PGA_scaffold4__129_contigs__length_65288255	LN:65288255
skipping SAM header line:	@SQ	SN:PGA_scaffold5__109_contigs__length_67248332	LN:67248332
skipping SAM header line:	@SQ	SN:PGA_scaffold6__104_contigs__length_61759565	LN:61759565
skipping SAM header line:	@SQ	SN:PGA_scaffold7__69_contigs__length_43120122	LN:43120122
skipping SAM header line:	@SQ	SN:PGA_scaffold8__63_contigs__length_61151155	LN:61151155
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skipping SAM header line:	@SQ	SN:PGA_scaffold12__71_contigs__length_50438331	LN:50438331
skipping SAM header line:	@SQ	SN:PGA_scaffold13__52_contigs__length_44396874	LN:44396874
skipping SAM header line:	@SQ	SN:PGA_scaffold14__91_contigs__length_45393038	LN:45393038
skipping SAM header line:	@SQ	SN:PGA_scaffold15__101_contigs__length_47938513	LN:47938513
skipping SAM header line:	@SQ	SN:PGA_scaffold16__33_contigs__length_31980953	LN:31980953
skipping SAM header line:	@SQ	SN:PGA_scaffold17__51_contigs__length_34923512	LN:34923512
skipping SAM header line:	@SQ	SN:PGA_scaffold18__69_contigs__length_27737463	LN:27737463
skipping SAM header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64 --samtools_path /gscratch/srlab/programs/samtools-1.9 --score_min L,0,-1.2 -I 60 -p 4 --genome /gscratch/srlab/sr320/data/geoduck/v074 -1 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R1_001_val_1.fq.gz -2 /gscratch/scrubbed/strigg/Pgen_FQs/EPI-227_S35_L004_R2_001_val_2.fq.gz -o /gscratch/scrubbed/strigg/analyses/20190806_v074"
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Merging individual splitting reports into overall report: '/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt'
Merging from these individual files:

Processed 4920488 lines in total
Total number of methylation call strings processed: 9840976

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	107719384

Total methylated C's in CpG context:	4102299
Total methylated C's in CHG context:	701005
Total methylated C's in CHH context:	5113731

Total C to T conversions in CpG context:	10164932
Total C to T conversions in CHG context:	21470747
Total C to T conversions in CHH context:	66166670

C methylated in CpG context:	28.8%
C methylated in CHG context:	3.2%
C methylated in CHH context:	7.2%



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: 101
Maximum read length of Read 2: 99

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: 101
Maximum read length of Read 2: 99

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/20190806_v074/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_CTOB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt was empty ->	deleted
/gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt contains data ->	kept


Using these input files: /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/strigg/analyses/20190806_v074/CHH_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
output directory:		>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
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: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz

Changed directory to /gscratch/scrubbed/strigg/analyses/20190806_v074/
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 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Finished writing methylation calls from CpG_OB_EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.txt to merged temp file
Sorting input file EPI-227_S35_L004_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 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...