*** Bismark methylation extractor version v0.23.1 ***

Trying to determine the type of mapping from the SAM header line of file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam
Treating file(s) as single-end data (as extracted from @PG line)

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

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 28
Output will be written to the current directory ('/gscratch/scrubbed/sr320/020122-CMoil')


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:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bam

skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.23.1	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -score_min L,0,-0.6 -non_directional -p 4 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gz"
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Now waiting for all child processes to complete
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Merging individual splitting reports into overall report: '20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.1
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.2
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.3
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.4
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.5
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.6
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.7
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.8
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.9
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.10
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.11
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.12
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.13
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.14
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.15
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.16
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.17
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.18
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.19
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.20
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.21
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.22
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.23
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.24
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.25
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.26
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.27
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 5189978 lines in total
Total number of methylation call strings processed: 5189978

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	100573067

Total methylated C's in CpG context:	12227583
Total methylated C's in CHG context:	5548341
Total methylated C's in CHH context:	18517042

Total C to T conversions in CpG context:	7392033
Total C to T conversions in CHG context:	18592605
Total C to T conversions in CHH context:	38295463

C methylated in CpG context:	62.3%
C methylated in CHG context:	23.0%
C methylated in CHH context:	32.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

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

CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/020122-CMoil/CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt

Writing bedGraph to file: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OB_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt


Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

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

Now reading in Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.23.1	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -score_min L,0,-0.6 -non_directional -p 4 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gz"
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
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Finished processing child process. Exiting..
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Finished processing child process. Exiting..
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Now waiting for all child processes to complete
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Merging individual splitting reports into overall report: '20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.1
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.2
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.3
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.4
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.5
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.6
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.7
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.8
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.9
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.10
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.11
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.12
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.13
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.14
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.15
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.16
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.17
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.18
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.19
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.20
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.21
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.22
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.23
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.24
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.25
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.26
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.27
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 8185761 lines in total
Total number of methylation call strings processed: 8185761

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	156364499

Total methylated C's in CpG context:	16759580
Total methylated C's in CHG context:	12344083
Total methylated C's in CHH context:	44317037

Total C to T conversions in CpG context:	8473982
Total C to T conversions in CHG context:	22151287
Total C to T conversions in CHH context:	52318530

C methylated in CpG context:	66.4%
C methylated in CHG context:	35.8%
C methylated in CHH context:	45.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

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

CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/020122-CMoil/CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt

Writing bedGraph to file: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OB_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt


Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam


Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam
Warning: unable to close filehandle IN properly.

Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.23.1	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -score_min L,0,-0.6 -non_directional -p 4 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz"
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Merging individual splitting reports into overall report: '20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.1
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.2
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.3
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.4
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.5
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.6
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.7
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.8
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.9
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.10
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.11
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.12
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.13
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.14
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.15
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.16
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.17
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.18
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.19
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.20
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.21
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.22
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.23
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.24
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.25
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.26
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.27
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 7626877 lines in total
Total number of methylation call strings processed: 7626877

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	149918833

Total methylated C's in CpG context:	18365481
Total methylated C's in CHG context:	12170718
Total methylated C's in CHH context:	41813087

Total C to T conversions in CpG context:	9333222
Total C to T conversions in CHG context:	22494040
Total C to T conversions in CHH context:	45742285

C methylated in CpG context:	66.3%
C methylated in CHG context:	35.1%
C methylated in CHH context:	47.8%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

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

CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/020122-CMoil/CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt

Writing bedGraph to file: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OB_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...

Checking file >>20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt


Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

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Now reading in Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bam

Warning: unable to close filehandle IN properly.
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping SAM header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping SAM header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping SAM header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping SAM header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping SAM header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping SAM header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping SAM header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping SAM header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping SAM header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping SAM header line:	@SQ	SN:NC_007175.2	LN:17244
skipping SAM header line:	@PG	ID:Bismark	VN:v0.23.1	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cvirg-genome/ -score_min L,0,-0.6 -non_directional -p 4 /gscratch/srlab/sr320/data/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gz"
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Merging individual splitting reports into overall report: '20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.1
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.2
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.3
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.4
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.5
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.6
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.7
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.8
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.9
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.10
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.11
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.12
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.13
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.14
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.15
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.16
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.17
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.18
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.19
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.20
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.21
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.22
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.23
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.24
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.25
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.26
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.27
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 5251301 lines in total
Total number of methylation call strings processed: 5251301

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	97243017

Total methylated C's in CpG context:	7983139
Total methylated C's in CHG context:	4299417
Total methylated C's in CHH context:	15816063

Total C to T conversions in CpG context:	9782238
Total C to T conversions in CHG context:	17880077
Total C to T conversions in CHH context:	41482083

C methylated in CpG context:	44.9%
C methylated in CHG context:	19.4%
C methylated in CHH context:	27.6%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table)
Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 101

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

CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt CHH_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
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:		75%
Coverage threshold:		1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

Using the following files as Input:
/gscratch/scrubbed/sr320/020122-CMoil/CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/sr320/020122-CMoil/CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt

Writing bedGraph to file: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bismark.cov.gz

Now writing methylation information for file >>CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_CTOB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt
Now writing methylation information for file >>CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt<< to individual files for each chromosome
Finished writing out individual chromosome files for CpG_OB_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt

Collecting temporary chromosome file information... Processing the following input file(s):
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp
CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_007175.2.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035780.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035781.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035782.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035783.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035784.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035785.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035786.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035787.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035788.1.methXtractor.temp

Sorting input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp by positions (using -S of 75%)
Successfully deleted the temporary input file CpG_OT_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.txt.chrNC_035789.1.methXtractor.temp

Finished BedGraph conversion ...