FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 100000 sequences in total

Sequences with no alignments under any condition:	71737
Sequences did not map uniquely:	9776
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	9334	((converted) top strand)
CT/GA:	9153	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	18487
Total number duplicated alignments removed:	29 (0.16%)
Duplicated alignments were found at:	26 different position(s)

Total count of deduplicated leftover sequences: 18458 (99.84% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 100000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_100000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 100000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Finished processing child process. Exiting..
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Now waiting for all child processes to complete

Merging individual splitting reports into overall report: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 18458 lines in total
Total number of methylation call strings processed: 18458

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	278472

Total methylated C's in CpG context:	29289
Total methylated C's in CHG context:	2395
Total methylated C's in CHH context:	18136

Total C to T conversions in CpG context:	9412
Total C to T conversions in CHG context:	55424
Total C to T conversions in CHH context:	163816

C methylated in CpG context:	75.7%
C methylated in CHG context:	4.1%
C methylated in CHH context:	10.0%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 76

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: 76

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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_100000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_100000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_100000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_100000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 500000 sequences in total

Sequences with no alignments under any condition:	357549
Sequences did not map uniquely:	49436
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	46787	((converted) top strand)
CT/GA:	46228	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	93015
Total number duplicated alignments removed:	531 (0.57%)
Duplicated alignments were found at:	454 different position(s)

Total count of deduplicated leftover sequences: 92484 (99.43% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 500000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_500000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 500000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Finished processing child process. Exiting..
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Merging individual splitting reports into overall report: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 92484 lines in total
Total number of methylation call strings processed: 92484

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	1392276

Total methylated C's in CpG context:	146724
Total methylated C's in CHG context:	11989
Total methylated C's in CHH context:	90098

Total C to T conversions in CpG context:	47087
Total C to T conversions in CHG context:	278276
Total C to T conversions in CHH context:	818102

C methylated in CpG context:	75.7%
C methylated in CHG context:	4.1%
C methylated in CHH context:	9.9%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 76

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: 76

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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_500000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_500000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_500000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_500000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 1000000 sequences in total

Sequences with no alignments under any condition:	705799
Sequences did not map uniquely:	102281
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	96405	((converted) top strand)
CT/GA:	95515	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	191920
Total number duplicated alignments removed:	1523 (0.79%)
Duplicated alignments were found at:	1240 different position(s)

Total count of deduplicated leftover sequences: 190397 (99.21% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 1000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_1000000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 1000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Finished processing child process. Exiting..
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Merging individual splitting reports into overall report: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 190397 lines in total
Total number of methylation call strings processed: 190397

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	2841113

Total methylated C's in CpG context:	295962
Total methylated C's in CHG context:	21717
Total methylated C's in CHH context:	164097

Total C to T conversions in CpG context:	96371
Total C to T conversions in CHG context:	569867
Total C to T conversions in CHH context:	1693099

C methylated in CpG context:	75.4%
C methylated in CHG context:	3.7%
C methylated in CHH context:	8.8%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 76

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: 76

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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_1000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_1000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_1000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_1000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 2000000 sequences in total

Sequences with no alignments under any condition:	1400838
Sequences did not map uniquely:	208674
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	195707	((converted) top strand)
CT/GA:	194781	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	390488
Total number duplicated alignments removed:	4757 (1.22%)
Duplicated alignments were found at:	3800 different position(s)

Total count of deduplicated leftover sequences: 385731 (98.78% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 2000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_2000000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 2000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Finished processing child process. Exiting..
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Merging individual splitting reports into overall report: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 385731 lines in total
Total number of methylation call strings processed: 385731

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	5745638

Total methylated C's in CpG context:	600246
Total methylated C's in CHG context:	40711
Total methylated C's in CHH context:	312080

Total C to T conversions in CpG context:	195545
Total C to T conversions in CHG context:	1163367
Total C to T conversions in CHH context:	3433689

C methylated in CpG context:	75.4%
C methylated in CHG context:	3.4%
C methylated in CHH context:	8.3%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 76

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: 76

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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_2000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_2000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_2000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_2000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 5000000 sequences in total

Sequences with no alignments under any condition:	3569125
Sequences did not map uniquely:	498819
Sequences which were discarded because genomic sequence could not be extracted:	0

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	465565	((converted) top strand)
CT/GA:	466491	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	932056
Total number duplicated alignments removed:	22562 (2.42%)
Duplicated alignments were found at:	17140 different position(s)

Total count of deduplicated leftover sequences: 909494 (97.58% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 5000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_5000000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 5000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Processed lines: 500000
Finished processing child process. Exiting..
Finished processing child process. Exiting..
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Finished processing child process. Exiting..
Now waiting for all child processes to complete
Finished processing child process. Exiting..
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Finished processing child process. Exiting..

Merging individual splitting reports into overall report: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 909494 lines in total
Total number of methylation call strings processed: 909494

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13496392

Total methylated C's in CpG context:	1360954
Total methylated C's in CHG context:	94075
Total methylated C's in CHH context:	737951

Total C to T conversions in CpG context:	527776
Total C to T conversions in CHG context:	2752388
Total C to T conversions in CHH context:	8023248

C methylated in CpG context:	72.1%
C methylated in CHG context:	3.3%
C methylated in CHH context:	8.4%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28.mbias

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 76

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: 76

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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_5000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_5000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_5000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_5000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...
FastQ format assumed (by default)
Each Bowtie 2 instance is going to be run with 28 threads. Please monitor performance closely and tune down if needed!
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Processed 10000000 sequences in total

Sequences with no alignments under any condition:	7479240
Sequences did not map uniquely:	907664
Sequences which were discarded because genomic sequence could not be extracted:	2

Number of sequences with unique best (first) alignment came from the bowtie output:
CT/CT:	810107	((converted) top strand)
CT/GA:	802987	((converted) bottom strand)
GA/CT:	0	(complementary to (converted) top strand)
GA/GA:	0	(complementary to (converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Processing single-end Bismark output file(s) (SAM format):
cvir_bsseq_all_R1_bismark_bt2.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>cvir_bsseq_all_R1_bismark_bt2.bam<< for signs of file truncation...


Output file is: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Total number of alignments analysed in cvir_bsseq_all_R1_bismark_bt2.bam:	1613094
Total number duplicated alignments removed:	104357 (6.47%)
Duplicated alignments were found at:	63570 different position(s)

Total count of deduplicated leftover sequences: 1508737 (93.53% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 10000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"

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

Trying to determine the type of mapping from the SAM header line of file cvir_bsseq_all_R1_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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000')


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)
White spaces in read ID names will be removed prior to sorting
The bedGraph UNIX sort command will use the following memory setting:	'75%'. Temporary directory used for sorting is the output directory

Checking file >>cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam


Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bam

Now reading in Bismark result file cvir_bsseq_all_R1_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:v0.19.0	CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ --genome /gscratch/srlab/sam/data/C_virginica/genomes/ --score_min L,0,-0.6 -u 10000000 -p 28 /gscratch/scrubbed/samwhite/data/C_virginica/BSseq/cvir_bsseq_all_R1.fastq.gz"
Processed lines: 500000
Processed lines: 500000
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Processed lines: 1000000
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Processed lines: 1500000
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: 'cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt'
Merging from these individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.28


Processed 1508737 lines in total
Total number of methylation call strings processed: 1508737

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	24639748

Total methylated C's in CpG context:	2709819
Total methylated C's in CHG context:	1260694
Total methylated C's in CHH context:	4840111

Total C to T conversions in CpG context:	956130
Total C to T conversions in CHG context:	3847573
Total C to T conversions in CHH context:	11025421

C methylated in CpG context:	73.9%
C methylated in CHG context:	24.7%
C methylated in CHH context:	30.5%



Merging individual M-bias reports into overall M-bias statistics from these 28 individual files:
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.1.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.2.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.3.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.4.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.5.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.6.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.7.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.8.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.9.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.10.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.11.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.12.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.13.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.14.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.15.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.16.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.17.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.18.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.19.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.20.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.21.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.22.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.23.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.24.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.25.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.26.mbias
cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt.27.mbias
cvir_bsseq_all_R1_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_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CpG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHG_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept
CHH_CTOT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_CTOB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt was empty ->	deleted
CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt contains data ->	kept


Using these input files: CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt CHH_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:		cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
output directory:		><
remove whitespaces:		yes
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/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt	/gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt

Writing bedGraph to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: cvir_bsseq_all_R1_bismark_bt2.deduplicated.bismark.cov.gz

The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files...
Writing all merged methylation calls to temp file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000/CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OT_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /gscratch/scrubbed/samwhite/outputs/20190222_cvirginica_se_bismark/subset_10000000/CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt prior to bedGraph conversion

Attempting to write to file CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt

Finished writing methylation calls from CpG_OB_cvir_bsseq_all_R1_bismark_bt2.deduplicated.txt.spaces_removed.txt to merged temp file
Sorting input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%)
Successfully deleted the temporary input file cvir_bsseq_all_R1_bismark_bt2.deduplicated.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

Found 1 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports

Writing Bismark HTML report to >> cvir_bsseq_all_R1_bismark_bt2_SE_report.html <<

==============================================================================================================
Using the following alignment report:		> cvir_bsseq_all_R1_bismark_bt2_SE_report.txt <
Processing alignment report cvir_bsseq_all_R1_bismark_bt2_SE_report.txt ...
Complete

Using the following deduplication report:	> cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt <
Processing deduplication report cvir_bsseq_all_R1_bismark_bt2.deduplication_report.txt ...
Complete

Using the following splitting report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt <
Processing splitting report cvir_bsseq_all_R1_bismark_bt2.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt <
Processing M-bias report cvir_bsseq_all_R1_bismark_bt2.deduplicated.M-bias.txt ...
Complete

No nucleotide coverage report file specified, skipping this step
==============================================================================================================


Found Bismark/Bowtie2 single-end files
No Bismark/Bowtie2 paired-end BAM files detected
No Bismark/Bowtie single-end BAM files detected
No Bismark/Bowtie paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: cvir_bsseq_all_R1_bismark_bt2_SE_report.txt

Wrote Bismark project summary to >> bismark_summary_report.html <<

[bam_sort_core] merging from 0 files and 28 in-memory blocks...