Bismark Methylation Extraction

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setwd("~/Documents/C-virginica-BSSeq/MethylationExtraction")
files <- list.files(pattern = "*.bam", path = ".")
for(i in 1:length(files))   {
  
  system(paste0("bismark_methylation_extractor --scaffolds --merge_non_CpG --bedGraph --zero_based ", files[i]))
  
}

 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
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skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
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skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
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skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
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skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
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skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
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skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
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skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
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skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_ACAGTG_L001_R1.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_ACAGTG"
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 3000000

Processed 3456338 lines in total
Total number of methylation call strings processed: 3456338

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   61813350

Total methylated C's in CpG context:    12572131
Total methylated C's in CHG context:    4005979
Total methylated C's in CHH context:    12350257

Total C to T conversions in CpG context:    2271987
Total C to T conversions in CHG context:    12442077
Total C to T conversions in CHH context:    18170919

C methylated in CpG context:    84.7%
C methylated in non-CpG context:    34.8%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->  kept
CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bam.txt contains data ->  kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_ACAGTG_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...


 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
skipping SAM header line:   @SQ SN:KV918245.1   LN:4832883
skipping SAM header line:   @SQ SN:KV918246.1   LN:4378960
skipping SAM header line:   @SQ SN:MWPT01000009.1   LN:3356639
skipping SAM header line:   @SQ SN:KV918247.1   LN:2355263
skipping SAM header line:   @SQ SN:KV918248.1   LN:3911507
skipping SAM header line:   @SQ SN:MWPT01000017.1   LN:2686679
skipping SAM header line:   @SQ SN:KV918249.1   LN:2829685
skipping SAM header line:   @SQ SN:KV918250.1   LN:3333291
skipping SAM header line:   @SQ SN:KV918251.1   LN:2850922
skipping SAM header line:   @SQ SN:KV918252.1   LN:5300508
skipping SAM header line:   @SQ SN:KV918253.1   LN:2652252
skipping SAM header line:   @SQ SN:KV918254.1   LN:3461433
skipping SAM header line:   @SQ SN:MWPT01000032.1   LN:1975305
skipping SAM header line:   @SQ SN:KV918255.1   LN:2606931
skipping SAM header line:   @SQ SN:MWPT01000041.1   LN:1717003
skipping SAM header line:   @SQ SN:KV918256.1   LN:2582953
skipping SAM header line:   @SQ SN:KV918257.1   LN:2738754
skipping SAM header line:   @SQ SN:MWPT01000052.1   LN:1062419
skipping SAM header line:   @SQ SN:KV918258.1   LN:1578002
skipping SAM header line:   @SQ SN:KV918259.1   LN:1347034
skipping SAM header line:   @SQ SN:KV918260.1   LN:684916
skipping SAM header line:   @SQ SN:MWPT01000061.1   LN:509886
skipping SAM header line:   @SQ SN:KV918261.1   LN:1120656
skipping SAM header line:   @SQ SN:MWPT01000067.1   LN:376046
skipping SAM header line:   @SQ SN:KV918262.1   LN:444482
skipping SAM header line:   @SQ SN:MWPT01000070.1   LN:357480
skipping SAM header line:   @SQ SN:MWPT01000071.1   LN:291238
skipping SAM header line:   @SQ SN:KV918263.1   LN:1230771
skipping SAM header line:   @SQ SN:MWPT01000527.1   LN:136883
skipping SAM header line:   @SQ SN:KV918264.1   LN:12680670
skipping SAM header line:   @SQ SN:KV918265.1   LN:2816827
skipping SAM header line:   @SQ SN:KV918266.1   LN:2977081
skipping SAM header line:   @SQ SN:MWPT01000137.1   LN:2796345
skipping SAM header line:   @SQ SN:MWPT01000138.1   LN:2693371
skipping SAM header line:   @SQ SN:MWPT01000139.1   LN:2365311
skipping SAM header line:   @SQ SN:MWPT01000140.1   LN:2238563
skipping SAM header line:   @SQ SN:MWPT01000141.1   LN:2207340
skipping SAM header line:   @SQ SN:KV918267.1   LN:2277360
skipping SAM header line:   @SQ SN:KV918268.1   LN:2822076
skipping SAM header line:   @SQ SN:KV918269.1   LN:3547160
skipping SAM header line:   @SQ SN:MWPT01000152.1   LN:1096595
skipping SAM header line:   @SQ SN:KV918270.1   LN:2145051
skipping SAM header line:   @SQ SN:KV918271.1   LN:1587102
skipping SAM header line:   @SQ SN:MWPT01000161.1   LN:1425844
skipping SAM header line:   @SQ SN:KV918272.1   LN:1907351
skipping SAM header line:   @SQ SN:MWPT01000166.1   LN:1422582
skipping SAM header line:   @SQ SN:KV918273.1   LN:1339065
skipping SAM header line:   @SQ SN:KV918274.1   LN:1546923
skipping SAM header line:   @SQ SN:KV918275.1   LN:1698010
skipping SAM header line:   @SQ SN:MWPT01000175.1   LN:1051837
skipping SAM header line:   @SQ SN:KV918276.1   LN:981967
skipping SAM header line:   @SQ SN:MWPT01000182.1   LN:448202
skipping SAM header line:   @SQ SN:KV918277.1   LN:917777
skipping SAM header line:   @SQ SN:MWPT01000185.1   LN:839050
skipping SAM header line:   @SQ SN:MWPT01000186.1   LN:724047
skipping SAM header line:   @SQ SN:MWPT01000187.1   LN:682532
skipping SAM header line:   @SQ SN:MWPT01000188.1   LN:392340
skipping SAM header line:   @SQ SN:MWPT01000189.1   LN:356808
skipping SAM header line:   @SQ SN:KV918278.1   LN:2436952
skipping SAM header line:   @SQ SN:KV918279.1   LN:385926
skipping SAM header line:   @SQ SN:KV918280.1   LN:1961913
skipping SAM header line:   @SQ SN:KV918281.1   LN:7786243
skipping SAM header line:   @SQ SN:MWPT01000194.1   LN:3534718
skipping SAM header line:   @SQ SN:MWPT01000195.1   LN:3254428
skipping SAM header line:   @SQ SN:MWPT01000196.1   LN:2889749
skipping SAM header line:   @SQ SN:MWPT01000197.1   LN:2524072
skipping SAM header line:   @SQ SN:MWPT01000198.1   LN:2141569
skipping SAM header line:   @SQ SN:MWPT01000199.1   LN:2045508
skipping SAM header line:   @SQ SN:KV918282.1   LN:2192831
skipping SAM header line:   @SQ SN:KV918283.1   LN:3982359
skipping SAM header line:   @SQ SN:MWPT01000205.1   LN:1913558
skipping SAM header line:   @SQ SN:KV918284.1   LN:5938325
skipping SAM header line:   @SQ SN:MWPT01000213.1   LN:1819665
skipping SAM header line:   @SQ SN:KV918285.1   LN:3010866
skipping SAM header line:   @SQ SN:MWPT01000216.1   LN:1543109
skipping SAM header line:   @SQ SN:KV918286.1   LN:1541268
skipping SAM header line:   @SQ SN:MWPT01000219.1   LN:1527358
skipping SAM header line:   @SQ SN:MWPT01000220.1   LN:927761
skipping SAM header line:   @SQ SN:KV918287.1   LN:1495603
skipping SAM header line:   @SQ SN:MWPT01000225.1   LN:1391987
skipping SAM header line:   @SQ SN:MWPT01000226.1   LN:1267255
skipping SAM header line:   @SQ SN:MWPT01000227.1   LN:1262423
skipping SAM header line:   @SQ SN:MWPT01000228.1   LN:1255886
skipping SAM header line:   @SQ SN:KV918288.1   LN:2059602
skipping SAM header line:   @SQ SN:MWPT01000236.1   LN:1098465
skipping SAM header line:   @SQ SN:MWPT01000237.1   LN:1081217
skipping SAM header line:   @SQ SN:KV918289.1   LN:1222516
skipping SAM header line:   @SQ SN:MWPT01000241.1   LN:1057763
skipping SAM header line:   @SQ SN:KV918290.1   LN:2056098
skipping SAM header line:   @SQ SN:KV918291.1   LN:1857027
skipping SAM header line:   @SQ SN:KV918292.1   LN:1203224
skipping SAM header line:   @SQ SN:MWPT01000254.1   LN:865943
skipping SAM header line:   @SQ SN:KV918293.1   LN:904861
skipping SAM header line:   @SQ SN:MWPT01000257.1   LN:843307
skipping SAM header line:   @SQ SN:MWPT01000258.1   LN:872954
skipping SAM header line:   @SQ SN:KV918294.1   LN:1445946
skipping SAM header line:   @SQ SN:MWPT01000261.1   LN:815299
skipping SAM header line:   @SQ SN:MWPT01000262.1   LN:819735
skipping SAM header line:   @SQ SN:KV918295.1   LN:894170
skipping SAM header line:   @SQ SN:MWPT01000266.1   LN:593101
skipping SAM header line:   @SQ SN:MWPT01000267.1   LN:517245
skipping SAM header line:   @SQ SN:MWPT01000268.1   LN:422393
skipping SAM header line:   @SQ SN:KV918296.1   LN:374206
skipping SAM header line:   @SQ SN:MWPT01000271.1   LN:285735
skipping SAM header line:   @SQ SN:KV918297.1   LN:2638124
skipping SAM header line:   @SQ SN:MWPT01000132.1   LN:3069683
skipping SAM header line:   @SQ SN:KV918298.1   LN:6258228
skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
skipping SAM header line:   @SQ SN:KV918300.1   LN:4909813
skipping SAM header line:   @SQ SN:KV918301.1   LN:4886044
skipping SAM header line:   @SQ SN:MWPT01000292.1   LN:3102771
skipping SAM header line:   @SQ SN:KV918302.1   LN:4906456
skipping SAM header line:   @SQ SN:KV918303.1   LN:2044046
skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
skipping SAM header line:   @SQ SN:MWPT01000305.1   LN:2187399
skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
skipping SAM header line:   @SQ SN:KV918307.1   LN:2308754
skipping SAM header line:   @SQ SN:KV918308.1   LN:1938434
skipping SAM header line:   @SQ SN:MWPT01000320.1   LN:1317752
skipping SAM header line:   @SQ SN:KV918309.1   LN:1352802
skipping SAM header line:   @SQ SN:KV918310.1   LN:2226218
skipping SAM header line:   @SQ SN:MWPT01000328.1   LN:1052579
skipping SAM header line:   @SQ SN:KV918311.1   LN:923568
skipping SAM header line:   @SQ SN:KV918312.1   LN:1134795
skipping SAM header line:   @SQ SN:MWPT01000334.1   LN:885077
skipping SAM header line:   @SQ SN:MWPT01000335.1   LN:824456
skipping SAM header line:   @SQ SN:MWPT01000336.1   LN:765637
skipping SAM header line:   @SQ SN:KV918313.1   LN:584168
skipping SAM header line:   @SQ SN:KV918314.1   LN:944098
skipping SAM header line:   @SQ SN:KV918315.1   LN:808456
skipping SAM header line:   @SQ SN:MWPT01000343.1   LN:482633
skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
skipping SAM header line:   @SQ SN:KV918317.1   LN:2074599
skipping SAM header line:   @SQ SN:KV918318.1   LN:9119220
skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
skipping SAM header line:   @SQ SN:MWPT01000351.1   LN:4187197
skipping SAM header line:   @SQ SN:KV918319.1   LN:4367352
skipping SAM header line:   @SQ SN:KV918320.1   LN:4548939
skipping SAM header line:   @SQ SN:KV918321.1   LN:3696092
skipping SAM header line:   @SQ SN:KV918322.1   LN:3948338
skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
skipping SAM header line:   @SQ SN:KV918323.1   LN:4044222
skipping SAM header line:   @SQ SN:MWPT01000363.1   LN:2689329
skipping SAM header line:   @SQ SN:KV918324.1   LN:2791483
skipping SAM header line:   @SQ SN:KV918325.1   LN:2940093
skipping SAM header line:   @SQ SN:KV918326.1   LN:2068281
skipping SAM header line:   @SQ SN:KV918327.1   LN:2465851
skipping SAM header line:   @SQ SN:MWPT01000378.1   LN:748885
skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
skipping SAM header line:   @SQ SN:KV918330.1   LN:709582
skipping SAM header line:   @SQ SN:KV918331.1   LN:1455932
skipping SAM header line:   @SQ SN:KV918332.1   LN:5224090
skipping SAM header line:   @SQ SN:KV918333.1   LN:10098079
skipping SAM header line:   @SQ SN:KV918334.1   LN:10066667
skipping SAM header line:   @SQ SN:KV918335.1   LN:6231318
skipping SAM header line:   @SQ SN:MWPT01000396.1   LN:3199022
skipping SAM header line:   @SQ SN:MWPT01000398.1   LN:3334036
skipping SAM header line:   @SQ SN:MWPT01000403.1   LN:3473365
skipping SAM header line:   @SQ SN:MWPT01000404.1   LN:3037733
skipping SAM header line:   @SQ SN:MWPT01000405.1   LN:2721753
skipping SAM header line:   @SQ SN:KV918336.1   LN:2171808
skipping SAM header line:   @SQ SN:KV918337.1   LN:1620111
skipping SAM header line:   @SQ SN:KV918338.1   LN:1605531
skipping SAM header line:   @SQ SN:MWPT01000413.1   LN:509639
skipping SAM header line:   @SQ SN:KV918339.1   LN:166177
skipping SAM header line:   @SQ SN:KV918340.1   LN:592233
skipping SAM header line:   @SQ SN:MWPT01000012.1   LN:656707
skipping SAM header line:   @SQ SN:KV918341.1   LN:2281237
skipping SAM header line:   @SQ SN:MWPT01000416.1   LN:3228757
skipping SAM header line:   @SQ SN:MWPT01000417.1   LN:3070944
skipping SAM header line:   @SQ SN:MWPT01000418.1   LN:2999364
skipping SAM header line:   @SQ SN:KV918342.1   LN:2965468
skipping SAM header line:   @SQ SN:KV918343.1   LN:4001099
skipping SAM header line:   @SQ SN:KV918344.1   LN:2468544
skipping SAM header line:   @SQ SN:KV918345.1   LN:3799038
skipping SAM header line:   @SQ SN:MWPT01000430.1   LN:2027284
skipping SAM header line:   @SQ SN:KV918346.1   LN:2335779
skipping SAM header line:   @SQ SN:MWPT01000433.1   LN:1832700
skipping SAM header line:   @SQ SN:KV918347.1   LN:1755862
skipping SAM header line:   @SQ SN:KV918348.1   LN:1786188
skipping SAM header line:   @SQ SN:MWPT01000439.1   LN:1596044
skipping SAM header line:   @SQ SN:MWPT01000440.1   LN:1470869
skipping SAM header line:   @SQ SN:KV918349.1   LN:1124868
skipping SAM header line:   @SQ SN:MWPT01000446.1   LN:1358169
skipping SAM header line:   @SQ SN:MWPT01000447.1   LN:1303672
skipping SAM header line:   @SQ SN:MWPT01000448.1   LN:1292038
skipping SAM header line:   @SQ SN:KV918350.1   LN:2216547
skipping SAM header line:   @SQ SN:KV918351.1   LN:2144614
skipping SAM header line:   @SQ SN:KV918352.1   LN:2200068
skipping SAM header line:   @SQ SN:MWPT01000458.1   LN:1154801
skipping SAM header line:   @SQ SN:KV918353.1   LN:1249097
skipping SAM header line:   @SQ SN:MWPT01000461.1   LN:1054511
skipping SAM header line:   @SQ SN:MWPT01000462.1   LN:1029825
skipping SAM header line:   @SQ SN:KV918354.1   LN:1474778
skipping SAM header line:   @SQ SN:KV918355.1   LN:1882473
skipping SAM header line:   @SQ SN:KV918356.1   LN:1195088
skipping SAM header line:   @SQ SN:KV918357.1   LN:945790
skipping SAM header line:   @SQ SN:MWPT01000471.1   LN:901603
skipping SAM header line:   @SQ SN:MWPT01000472.1   LN:883242
skipping SAM header line:   @SQ SN:MWPT01000473.1   LN:863120
skipping SAM header line:   @SQ SN:KV918358.1   LN:906525
skipping SAM header line:   @SQ SN:KV918359.1   LN:1452728
skipping SAM header line:   @SQ SN:MWPT01000480.1   LN:748682
skipping SAM header line:   @SQ SN:KV918360.1   LN:659974
skipping SAM header line:   @SQ SN:KV918361.1   LN:466019
skipping SAM header line:   @SQ SN:MWPT01000013.1   LN:1300831
skipping SAM header line:   @SQ SN:MWPT01000131.1   LN:1971208
skipping SAM header line:   @SQ SN:KV918362.1   LN:2791541
skipping SAM header line:   @SQ SN:KV918363.1   LN:1907303
skipping SAM header line:   @SQ SN:MWPT01000397.1   LN:1723226
skipping SAM header line:   @SQ SN:MWPT01000410.1   LN:500894
skipping SAM header line:   @SQ SN:KV918364.1   LN:6892396
skipping SAM header line:   @SQ SN:KV918365.1   LN:7468933
skipping SAM header line:   @SQ SN:MWPT01000490.1   LN:3601090
skipping SAM header line:   @SQ SN:MWPT01000491.1   LN:2581635
skipping SAM header line:   @SQ SN:MWPT01000492.1   LN:2281164
skipping SAM header line:   @SQ SN:KV918366.1   LN:3576272
skipping SAM header line:   @SQ SN:KV918367.1   LN:3792723
skipping SAM header line:   @SQ SN:KV918368.1   LN:2247201
skipping SAM header line:   @SQ SN:KV918369.1   LN:2662616
skipping SAM header line:   @SQ SN:KV918370.1   LN:2530331
skipping SAM header line:   @SQ SN:MWPT01000510.1   LN:1983864
skipping SAM header line:   @SQ SN:KV918371.1   LN:1956835
skipping SAM header line:   @SQ SN:KV918372.1   LN:3086374
skipping SAM header line:   @SQ SN:KV918373.1   LN:3420601
skipping SAM header line:   @SQ SN:KV918374.1   LN:1975111
skipping SAM header line:   @SQ SN:MWPT01000522.1   LN:1408919
skipping SAM header line:   @SQ SN:KV918375.1   LN:2529433
skipping SAM header line:   @SQ SN:KV918376.1   LN:1290748
skipping SAM header line:   @SQ SN:KV918377.1   LN:2437656
skipping SAM header line:   @SQ SN:MWPT01000531.1   LN:1154204
skipping SAM header line:   @SQ SN:KV918378.1   LN:1139503
skipping SAM header line:   @SQ SN:MWPT01000536.1   LN:868008
skipping SAM header line:   @SQ SN:MWPT01000537.1   LN:771245
skipping SAM header line:   @SQ SN:KV918379.1   LN:1322005
skipping SAM header line:   @SQ SN:KV918380.1   LN:1966111
skipping SAM header line:   @SQ SN:MWPT01000546.1   LN:662674
skipping SAM header line:   @SQ SN:KV918381.1   LN:1109647
skipping SAM header line:   @SQ SN:KV918382.1   LN:871299
skipping SAM header line:   @SQ SN:MWPT01000551.1   LN:451986
skipping SAM header line:   @SQ SN:MWPT01000552.1   LN:323820
skipping SAM header line:   @SQ SN:MWPT01000553.1   LN:248130
skipping SAM header line:   @SQ SN:MWPT01000240.1   LN:21598
skipping SAM header line:   @SQ SN:KV918383.1   LN:3521928
skipping SAM header line:   @SQ SN:KV918384.1   LN:978841
skipping SAM header line:   @SQ SN:KV918385.1   LN:9025367
skipping SAM header line:   @SQ SN:MWPT01000562.1   LN:6788731
skipping SAM header line:   @SQ SN:MWPT01000563.1   LN:4429963
skipping SAM header line:   @SQ SN:KV918386.1   LN:3718566
skipping SAM header line:   @SQ SN:MWPT01000566.1   LN:2001120
skipping SAM header line:   @SQ SN:MWPT01000567.1   LN:1613306
skipping SAM header line:   @SQ SN:MWPT01000568.1   LN:1271813
skipping SAM header line:   @SQ SN:MWPT01000569.1   LN:1139655
skipping SAM header line:   @SQ SN:KV918387.1   LN:1748706
skipping SAM header line:   @SQ SN:KV918388.1   LN:1215097
skipping SAM header line:   @SQ SN:KV918389.1   LN:1703051
skipping SAM header line:   @SQ SN:MWPT01000577.1   LN:293636
skipping SAM header line:   @SQ SN:MWPT01000578.1   LN:295967
skipping SAM header line:   @SQ SN:MWPT01000072.1   LN:5034843
skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_ATCACG_R1.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_ATCACG"
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 8000000

Processed 8155789 lines in total
Total number of methylation call strings processed: 8155789

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   138933301

Total methylated C's in CpG context:    16732030
Total methylated C's in CHG context:    8219901
Total methylated C's in CHH context:    27822848

Total C to T conversions in CpG context:    6334489
Total C to T conversions in CHG context:    25074426
Total C to T conversions in CHH context:    54749607

C methylated in CpG context:    72.5%
C methylated in non-CpG context:    31.1%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data ->   kept
CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data -> kept
CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data -> kept
CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data ->   kept
Non_CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data ->   kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data -> kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt contains data -> kept
Non_CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bam.txt contains data ->   kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt  /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt    /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt    /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_ATCACG_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...


 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
skipping SAM header line:   @SQ SN:KV918245.1   LN:4832883
skipping SAM header line:   @SQ SN:KV918246.1   LN:4378960
skipping SAM header line:   @SQ SN:MWPT01000009.1   LN:3356639
skipping SAM header line:   @SQ SN:KV918247.1   LN:2355263
skipping SAM header line:   @SQ SN:KV918248.1   LN:3911507
skipping SAM header line:   @SQ SN:MWPT01000017.1   LN:2686679
skipping SAM header line:   @SQ SN:KV918249.1   LN:2829685
skipping SAM header line:   @SQ SN:KV918250.1   LN:3333291
skipping SAM header line:   @SQ SN:KV918251.1   LN:2850922
skipping SAM header line:   @SQ SN:KV918252.1   LN:5300508
skipping SAM header line:   @SQ SN:KV918253.1   LN:2652252
skipping SAM header line:   @SQ SN:KV918254.1   LN:3461433
skipping SAM header line:   @SQ SN:MWPT01000032.1   LN:1975305
skipping SAM header line:   @SQ SN:KV918255.1   LN:2606931
skipping SAM header line:   @SQ SN:MWPT01000041.1   LN:1717003
skipping SAM header line:   @SQ SN:KV918256.1   LN:2582953
skipping SAM header line:   @SQ SN:KV918257.1   LN:2738754
skipping SAM header line:   @SQ SN:MWPT01000052.1   LN:1062419
skipping SAM header line:   @SQ SN:KV918258.1   LN:1578002
skipping SAM header line:   @SQ SN:KV918259.1   LN:1347034
skipping SAM header line:   @SQ SN:KV918260.1   LN:684916
skipping SAM header line:   @SQ SN:MWPT01000061.1   LN:509886
skipping SAM header line:   @SQ SN:KV918261.1   LN:1120656
skipping SAM header line:   @SQ SN:MWPT01000067.1   LN:376046
skipping SAM header line:   @SQ SN:KV918262.1   LN:444482
skipping SAM header line:   @SQ SN:MWPT01000070.1   LN:357480
skipping SAM header line:   @SQ SN:MWPT01000071.1   LN:291238
skipping SAM header line:   @SQ SN:KV918263.1   LN:1230771
skipping SAM header line:   @SQ SN:MWPT01000527.1   LN:136883
skipping SAM header line:   @SQ SN:KV918264.1   LN:12680670
skipping SAM header line:   @SQ SN:KV918265.1   LN:2816827
skipping SAM header line:   @SQ SN:KV918266.1   LN:2977081
skipping SAM header line:   @SQ SN:MWPT01000137.1   LN:2796345
skipping SAM header line:   @SQ SN:MWPT01000138.1   LN:2693371
skipping SAM header line:   @SQ SN:MWPT01000139.1   LN:2365311
skipping SAM header line:   @SQ SN:MWPT01000140.1   LN:2238563
skipping SAM header line:   @SQ SN:MWPT01000141.1   LN:2207340
skipping SAM header line:   @SQ SN:KV918267.1   LN:2277360
skipping SAM header line:   @SQ SN:KV918268.1   LN:2822076
skipping SAM header line:   @SQ SN:KV918269.1   LN:3547160
skipping SAM header line:   @SQ SN:MWPT01000152.1   LN:1096595
skipping SAM header line:   @SQ SN:KV918270.1   LN:2145051
skipping SAM header line:   @SQ SN:KV918271.1   LN:1587102
skipping SAM header line:   @SQ SN:MWPT01000161.1   LN:1425844
skipping SAM header line:   @SQ SN:KV918272.1   LN:1907351
skipping SAM header line:   @SQ SN:MWPT01000166.1   LN:1422582
skipping SAM header line:   @SQ SN:KV918273.1   LN:1339065
skipping SAM header line:   @SQ SN:KV918274.1   LN:1546923
skipping SAM header line:   @SQ SN:KV918275.1   LN:1698010
skipping SAM header line:   @SQ SN:MWPT01000175.1   LN:1051837
skipping SAM header line:   @SQ SN:KV918276.1   LN:981967
skipping SAM header line:   @SQ SN:MWPT01000182.1   LN:448202
skipping SAM header line:   @SQ SN:KV918277.1   LN:917777
skipping SAM header line:   @SQ SN:MWPT01000185.1   LN:839050
skipping SAM header line:   @SQ SN:MWPT01000186.1   LN:724047
skipping SAM header line:   @SQ SN:MWPT01000187.1   LN:682532
skipping SAM header line:   @SQ SN:MWPT01000188.1   LN:392340
skipping SAM header line:   @SQ SN:MWPT01000189.1   LN:356808
skipping SAM header line:   @SQ SN:KV918278.1   LN:2436952
skipping SAM header line:   @SQ SN:KV918279.1   LN:385926
skipping SAM header line:   @SQ SN:KV918280.1   LN:1961913
skipping SAM header line:   @SQ SN:KV918281.1   LN:7786243
skipping SAM header line:   @SQ SN:MWPT01000194.1   LN:3534718
skipping SAM header line:   @SQ SN:MWPT01000195.1   LN:3254428
skipping SAM header line:   @SQ SN:MWPT01000196.1   LN:2889749
skipping SAM header line:   @SQ SN:MWPT01000197.1   LN:2524072
skipping SAM header line:   @SQ SN:MWPT01000198.1   LN:2141569
skipping SAM header line:   @SQ SN:MWPT01000199.1   LN:2045508
skipping SAM header line:   @SQ SN:KV918282.1   LN:2192831
skipping SAM header line:   @SQ SN:KV918283.1   LN:3982359
skipping SAM header line:   @SQ SN:MWPT01000205.1   LN:1913558
skipping SAM header line:   @SQ SN:KV918284.1   LN:5938325
skipping SAM header line:   @SQ SN:MWPT01000213.1   LN:1819665
skipping SAM header line:   @SQ SN:KV918285.1   LN:3010866
skipping SAM header line:   @SQ SN:MWPT01000216.1   LN:1543109
skipping SAM header line:   @SQ SN:KV918286.1   LN:1541268
skipping SAM header line:   @SQ SN:MWPT01000219.1   LN:1527358
skipping SAM header line:   @SQ SN:MWPT01000220.1   LN:927761
skipping SAM header line:   @SQ SN:KV918287.1   LN:1495603
skipping SAM header line:   @SQ SN:MWPT01000225.1   LN:1391987
skipping SAM header line:   @SQ SN:MWPT01000226.1   LN:1267255
skipping SAM header line:   @SQ SN:MWPT01000227.1   LN:1262423
skipping SAM header line:   @SQ SN:MWPT01000228.1   LN:1255886
skipping SAM header line:   @SQ SN:KV918288.1   LN:2059602
skipping SAM header line:   @SQ SN:MWPT01000236.1   LN:1098465
skipping SAM header line:   @SQ SN:MWPT01000237.1   LN:1081217
skipping SAM header line:   @SQ SN:KV918289.1   LN:1222516
skipping SAM header line:   @SQ SN:MWPT01000241.1   LN:1057763
skipping SAM header line:   @SQ SN:KV918290.1   LN:2056098
skipping SAM header line:   @SQ SN:KV918291.1   LN:1857027
skipping SAM header line:   @SQ SN:KV918292.1   LN:1203224
skipping SAM header line:   @SQ SN:MWPT01000254.1   LN:865943
skipping SAM header line:   @SQ SN:KV918293.1   LN:904861
skipping SAM header line:   @SQ SN:MWPT01000257.1   LN:843307
skipping SAM header line:   @SQ SN:MWPT01000258.1   LN:872954
skipping SAM header line:   @SQ SN:KV918294.1   LN:1445946
skipping SAM header line:   @SQ SN:MWPT01000261.1   LN:815299
skipping SAM header line:   @SQ SN:MWPT01000262.1   LN:819735
skipping SAM header line:   @SQ SN:KV918295.1   LN:894170
skipping SAM header line:   @SQ SN:MWPT01000266.1   LN:593101
skipping SAM header line:   @SQ SN:MWPT01000267.1   LN:517245
skipping SAM header line:   @SQ SN:MWPT01000268.1   LN:422393
skipping SAM header line:   @SQ SN:KV918296.1   LN:374206
skipping SAM header line:   @SQ SN:MWPT01000271.1   LN:285735
skipping SAM header line:   @SQ SN:KV918297.1   LN:2638124
skipping SAM header line:   @SQ SN:MWPT01000132.1   LN:3069683
skipping SAM header line:   @SQ SN:KV918298.1   LN:6258228
skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
skipping SAM header line:   @SQ SN:KV918300.1   LN:4909813
skipping SAM header line:   @SQ SN:KV918301.1   LN:4886044
skipping SAM header line:   @SQ SN:MWPT01000292.1   LN:3102771
skipping SAM header line:   @SQ SN:KV918302.1   LN:4906456
skipping SAM header line:   @SQ SN:KV918303.1   LN:2044046
skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
skipping SAM header line:   @SQ SN:MWPT01000305.1   LN:2187399
skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
skipping SAM header line:   @SQ SN:KV918307.1   LN:2308754
skipping SAM header line:   @SQ SN:KV918308.1   LN:1938434
skipping SAM header line:   @SQ SN:MWPT01000320.1   LN:1317752
skipping SAM header line:   @SQ SN:KV918309.1   LN:1352802
skipping SAM header line:   @SQ SN:KV918310.1   LN:2226218
skipping SAM header line:   @SQ SN:MWPT01000328.1   LN:1052579
skipping SAM header line:   @SQ SN:KV918311.1   LN:923568
skipping SAM header line:   @SQ SN:KV918312.1   LN:1134795
skipping SAM header line:   @SQ SN:MWPT01000334.1   LN:885077
skipping SAM header line:   @SQ SN:MWPT01000335.1   LN:824456
skipping SAM header line:   @SQ SN:MWPT01000336.1   LN:765637
skipping SAM header line:   @SQ SN:KV918313.1   LN:584168
skipping SAM header line:   @SQ SN:KV918314.1   LN:944098
skipping SAM header line:   @SQ SN:KV918315.1   LN:808456
skipping SAM header line:   @SQ SN:MWPT01000343.1   LN:482633
skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
skipping SAM header line:   @SQ SN:KV918317.1   LN:2074599
skipping SAM header line:   @SQ SN:KV918318.1   LN:9119220
skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
skipping SAM header line:   @SQ SN:MWPT01000351.1   LN:4187197
skipping SAM header line:   @SQ SN:KV918319.1   LN:4367352
skipping SAM header line:   @SQ SN:KV918320.1   LN:4548939
skipping SAM header line:   @SQ SN:KV918321.1   LN:3696092
skipping SAM header line:   @SQ SN:KV918322.1   LN:3948338
skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
skipping SAM header line:   @SQ SN:KV918323.1   LN:4044222
skipping SAM header line:   @SQ SN:MWPT01000363.1   LN:2689329
skipping SAM header line:   @SQ SN:KV918324.1   LN:2791483
skipping SAM header line:   @SQ SN:KV918325.1   LN:2940093
skipping SAM header line:   @SQ SN:KV918326.1   LN:2068281
skipping SAM header line:   @SQ SN:KV918327.1   LN:2465851
skipping SAM header line:   @SQ SN:MWPT01000378.1   LN:748885
skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
skipping SAM header line:   @SQ SN:KV918330.1   LN:709582
skipping SAM header line:   @SQ SN:KV918331.1   LN:1455932
skipping SAM header line:   @SQ SN:KV918332.1   LN:5224090
skipping SAM header line:   @SQ SN:KV918333.1   LN:10098079
skipping SAM header line:   @SQ SN:KV918334.1   LN:10066667
skipping SAM header line:   @SQ SN:KV918335.1   LN:6231318
skipping SAM header line:   @SQ SN:MWPT01000396.1   LN:3199022
skipping SAM header line:   @SQ SN:MWPT01000398.1   LN:3334036
skipping SAM header line:   @SQ SN:MWPT01000403.1   LN:3473365
skipping SAM header line:   @SQ SN:MWPT01000404.1   LN:3037733
skipping SAM header line:   @SQ SN:MWPT01000405.1   LN:2721753
skipping SAM header line:   @SQ SN:KV918336.1   LN:2171808
skipping SAM header line:   @SQ SN:KV918337.1   LN:1620111
skipping SAM header line:   @SQ SN:KV918338.1   LN:1605531
skipping SAM header line:   @SQ SN:MWPT01000413.1   LN:509639
skipping SAM header line:   @SQ SN:KV918339.1   LN:166177
skipping SAM header line:   @SQ SN:KV918340.1   LN:592233
skipping SAM header line:   @SQ SN:MWPT01000012.1   LN:656707
skipping SAM header line:   @SQ SN:KV918341.1   LN:2281237
skipping SAM header line:   @SQ SN:MWPT01000416.1   LN:3228757
skipping SAM header line:   @SQ SN:MWPT01000417.1   LN:3070944
skipping SAM header line:   @SQ SN:MWPT01000418.1   LN:2999364
skipping SAM header line:   @SQ SN:KV918342.1   LN:2965468
skipping SAM header line:   @SQ SN:KV918343.1   LN:4001099
skipping SAM header line:   @SQ SN:KV918344.1   LN:2468544
skipping SAM header line:   @SQ SN:KV918345.1   LN:3799038
skipping SAM header line:   @SQ SN:MWPT01000430.1   LN:2027284
skipping SAM header line:   @SQ SN:KV918346.1   LN:2335779
skipping SAM header line:   @SQ SN:MWPT01000433.1   LN:1832700
skipping SAM header line:   @SQ SN:KV918347.1   LN:1755862
skipping SAM header line:   @SQ SN:KV918348.1   LN:1786188
skipping SAM header line:   @SQ SN:MWPT01000439.1   LN:1596044
skipping SAM header line:   @SQ SN:MWPT01000440.1   LN:1470869
skipping SAM header line:   @SQ SN:KV918349.1   LN:1124868
skipping SAM header line:   @SQ SN:MWPT01000446.1   LN:1358169
skipping SAM header line:   @SQ SN:MWPT01000447.1   LN:1303672
skipping SAM header line:   @SQ SN:MWPT01000448.1   LN:1292038
skipping SAM header line:   @SQ SN:KV918350.1   LN:2216547
skipping SAM header line:   @SQ SN:KV918351.1   LN:2144614
skipping SAM header line:   @SQ SN:KV918352.1   LN:2200068
skipping SAM header line:   @SQ SN:MWPT01000458.1   LN:1154801
skipping SAM header line:   @SQ SN:KV918353.1   LN:1249097
skipping SAM header line:   @SQ SN:MWPT01000461.1   LN:1054511
skipping SAM header line:   @SQ SN:MWPT01000462.1   LN:1029825
skipping SAM header line:   @SQ SN:KV918354.1   LN:1474778
skipping SAM header line:   @SQ SN:KV918355.1   LN:1882473
skipping SAM header line:   @SQ SN:KV918356.1   LN:1195088
skipping SAM header line:   @SQ SN:KV918357.1   LN:945790
skipping SAM header line:   @SQ SN:MWPT01000471.1   LN:901603
skipping SAM header line:   @SQ SN:MWPT01000472.1   LN:883242
skipping SAM header line:   @SQ SN:MWPT01000473.1   LN:863120
skipping SAM header line:   @SQ SN:KV918358.1   LN:906525
skipping SAM header line:   @SQ SN:KV918359.1   LN:1452728
skipping SAM header line:   @SQ SN:MWPT01000480.1   LN:748682
skipping SAM header line:   @SQ SN:KV918360.1   LN:659974
skipping SAM header line:   @SQ SN:KV918361.1   LN:466019
skipping SAM header line:   @SQ SN:MWPT01000013.1   LN:1300831
skipping SAM header line:   @SQ SN:MWPT01000131.1   LN:1971208
skipping SAM header line:   @SQ SN:KV918362.1   LN:2791541
skipping SAM header line:   @SQ SN:KV918363.1   LN:1907303
skipping SAM header line:   @SQ SN:MWPT01000397.1   LN:1723226
skipping SAM header line:   @SQ SN:MWPT01000410.1   LN:500894
skipping SAM header line:   @SQ SN:KV918364.1   LN:6892396
skipping SAM header line:   @SQ SN:KV918365.1   LN:7468933
skipping SAM header line:   @SQ SN:MWPT01000490.1   LN:3601090
skipping SAM header line:   @SQ SN:MWPT01000491.1   LN:2581635
skipping SAM header line:   @SQ SN:MWPT01000492.1   LN:2281164
skipping SAM header line:   @SQ SN:KV918366.1   LN:3576272
skipping SAM header line:   @SQ SN:KV918367.1   LN:3792723
skipping SAM header line:   @SQ SN:KV918368.1   LN:2247201
skipping SAM header line:   @SQ SN:KV918369.1   LN:2662616
skipping SAM header line:   @SQ SN:KV918370.1   LN:2530331
skipping SAM header line:   @SQ SN:MWPT01000510.1   LN:1983864
skipping SAM header line:   @SQ SN:KV918371.1   LN:1956835
skipping SAM header line:   @SQ SN:KV918372.1   LN:3086374
skipping SAM header line:   @SQ SN:KV918373.1   LN:3420601
skipping SAM header line:   @SQ SN:KV918374.1   LN:1975111
skipping SAM header line:   @SQ SN:MWPT01000522.1   LN:1408919
skipping SAM header line:   @SQ SN:KV918375.1   LN:2529433
skipping SAM header line:   @SQ SN:KV918376.1   LN:1290748
skipping SAM header line:   @SQ SN:KV918377.1   LN:2437656
skipping SAM header line:   @SQ SN:MWPT01000531.1   LN:1154204
skipping SAM header line:   @SQ SN:KV918378.1   LN:1139503
skipping SAM header line:   @SQ SN:MWPT01000536.1   LN:868008
skipping SAM header line:   @SQ SN:MWPT01000537.1   LN:771245
skipping SAM header line:   @SQ SN:KV918379.1   LN:1322005
skipping SAM header line:   @SQ SN:KV918380.1   LN:1966111
skipping SAM header line:   @SQ SN:MWPT01000546.1   LN:662674
skipping SAM header line:   @SQ SN:KV918381.1   LN:1109647
skipping SAM header line:   @SQ SN:KV918382.1   LN:871299
skipping SAM header line:   @SQ SN:MWPT01000551.1   LN:451986
skipping SAM header line:   @SQ SN:MWPT01000552.1   LN:323820
skipping SAM header line:   @SQ SN:MWPT01000553.1   LN:248130
skipping SAM header line:   @SQ SN:MWPT01000240.1   LN:21598
skipping SAM header line:   @SQ SN:KV918383.1   LN:3521928
skipping SAM header line:   @SQ SN:KV918384.1   LN:978841
skipping SAM header line:   @SQ SN:KV918385.1   LN:9025367
skipping SAM header line:   @SQ SN:MWPT01000562.1   LN:6788731
skipping SAM header line:   @SQ SN:MWPT01000563.1   LN:4429963
skipping SAM header line:   @SQ SN:KV918386.1   LN:3718566
skipping SAM header line:   @SQ SN:MWPT01000566.1   LN:2001120
skipping SAM header line:   @SQ SN:MWPT01000567.1   LN:1613306
skipping SAM header line:   @SQ SN:MWPT01000568.1   LN:1271813
skipping SAM header line:   @SQ SN:MWPT01000569.1   LN:1139655
skipping SAM header line:   @SQ SN:KV918387.1   LN:1748706
skipping SAM header line:   @SQ SN:KV918388.1   LN:1215097
skipping SAM header line:   @SQ SN:KV918389.1   LN:1703051
skipping SAM header line:   @SQ SN:MWPT01000577.1   LN:293636
skipping SAM header line:   @SQ SN:MWPT01000578.1   LN:295967
skipping SAM header line:   @SQ SN:MWPT01000072.1   LN:5034843
skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_CAGATC_R1.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_CAGATC"
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 6000000
Processed lines: 6500000
Processed lines: 7000000
Processed lines: 7500000
Processed lines: 8000000
Processed lines: 8500000
Processed lines: 9000000
Processed lines: 9500000

Processed 9511234 lines in total
Total number of methylation call strings processed: 9511234

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   164572332

Total methylated C's in CpG context:    24114043
Total methylated C's in CHG context:    8673987
Total methylated C's in CHH context:    27617213

Total C to T conversions in CpG context:    8682937
Total C to T conversions in CHG context:    33543424
Total C to T conversions in CHH context:    61940728

C methylated in CpG context:    73.5%
C methylated in non-CpG context:    27.5%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data ->   kept
CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data -> kept
CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data -> kept
CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data ->   kept
Non_CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data ->   kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data -> kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt contains data -> kept
Non_CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bam.txt contains data ->   kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt  /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt    /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt    /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_CAGATC_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...


 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
skipping SAM header line:   @SQ SN:KV918245.1   LN:4832883
skipping SAM header line:   @SQ SN:KV918246.1   LN:4378960
skipping SAM header line:   @SQ SN:MWPT01000009.1   LN:3356639
skipping SAM header line:   @SQ SN:KV918247.1   LN:2355263
skipping SAM header line:   @SQ SN:KV918248.1   LN:3911507
skipping SAM header line:   @SQ SN:MWPT01000017.1   LN:2686679
skipping SAM header line:   @SQ SN:KV918249.1   LN:2829685
skipping SAM header line:   @SQ SN:KV918250.1   LN:3333291
skipping SAM header line:   @SQ SN:KV918251.1   LN:2850922
skipping SAM header line:   @SQ SN:KV918252.1   LN:5300508
skipping SAM header line:   @SQ SN:KV918253.1   LN:2652252
skipping SAM header line:   @SQ SN:KV918254.1   LN:3461433
skipping SAM header line:   @SQ SN:MWPT01000032.1   LN:1975305
skipping SAM header line:   @SQ SN:KV918255.1   LN:2606931
skipping SAM header line:   @SQ SN:MWPT01000041.1   LN:1717003
skipping SAM header line:   @SQ SN:KV918256.1   LN:2582953
skipping SAM header line:   @SQ SN:KV918257.1   LN:2738754
skipping SAM header line:   @SQ SN:MWPT01000052.1   LN:1062419
skipping SAM header line:   @SQ SN:KV918258.1   LN:1578002
skipping SAM header line:   @SQ SN:KV918259.1   LN:1347034
skipping SAM header line:   @SQ SN:KV918260.1   LN:684916
skipping SAM header line:   @SQ SN:MWPT01000061.1   LN:509886
skipping SAM header line:   @SQ SN:KV918261.1   LN:1120656
skipping SAM header line:   @SQ SN:MWPT01000067.1   LN:376046
skipping SAM header line:   @SQ SN:KV918262.1   LN:444482
skipping SAM header line:   @SQ SN:MWPT01000070.1   LN:357480
skipping SAM header line:   @SQ SN:MWPT01000071.1   LN:291238
skipping SAM header line:   @SQ SN:KV918263.1   LN:1230771
skipping SAM header line:   @SQ SN:MWPT01000527.1   LN:136883
skipping SAM header line:   @SQ SN:KV918264.1   LN:12680670
skipping SAM header line:   @SQ SN:KV918265.1   LN:2816827
skipping SAM header line:   @SQ SN:KV918266.1   LN:2977081
skipping SAM header line:   @SQ SN:MWPT01000137.1   LN:2796345
skipping SAM header line:   @SQ SN:MWPT01000138.1   LN:2693371
skipping SAM header line:   @SQ SN:MWPT01000139.1   LN:2365311
skipping SAM header line:   @SQ SN:MWPT01000140.1   LN:2238563
skipping SAM header line:   @SQ SN:MWPT01000141.1   LN:2207340
skipping SAM header line:   @SQ SN:KV918267.1   LN:2277360
skipping SAM header line:   @SQ SN:KV918268.1   LN:2822076
skipping SAM header line:   @SQ SN:KV918269.1   LN:3547160
skipping SAM header line:   @SQ SN:MWPT01000152.1   LN:1096595
skipping SAM header line:   @SQ SN:KV918270.1   LN:2145051
skipping SAM header line:   @SQ SN:KV918271.1   LN:1587102
skipping SAM header line:   @SQ SN:MWPT01000161.1   LN:1425844
skipping SAM header line:   @SQ SN:KV918272.1   LN:1907351
skipping SAM header line:   @SQ SN:MWPT01000166.1   LN:1422582
skipping SAM header line:   @SQ SN:KV918273.1   LN:1339065
skipping SAM header line:   @SQ SN:KV918274.1   LN:1546923
skipping SAM header line:   @SQ SN:KV918275.1   LN:1698010
skipping SAM header line:   @SQ SN:MWPT01000175.1   LN:1051837
skipping SAM header line:   @SQ SN:KV918276.1   LN:981967
skipping SAM header line:   @SQ SN:MWPT01000182.1   LN:448202
skipping SAM header line:   @SQ SN:KV918277.1   LN:917777
skipping SAM header line:   @SQ SN:MWPT01000185.1   LN:839050
skipping SAM header line:   @SQ SN:MWPT01000186.1   LN:724047
skipping SAM header line:   @SQ SN:MWPT01000187.1   LN:682532
skipping SAM header line:   @SQ SN:MWPT01000188.1   LN:392340
skipping SAM header line:   @SQ SN:MWPT01000189.1   LN:356808
skipping SAM header line:   @SQ SN:KV918278.1   LN:2436952
skipping SAM header line:   @SQ SN:KV918279.1   LN:385926
skipping SAM header line:   @SQ SN:KV918280.1   LN:1961913
skipping SAM header line:   @SQ SN:KV918281.1   LN:7786243
skipping SAM header line:   @SQ SN:MWPT01000194.1   LN:3534718
skipping SAM header line:   @SQ SN:MWPT01000195.1   LN:3254428
skipping SAM header line:   @SQ SN:MWPT01000196.1   LN:2889749
skipping SAM header line:   @SQ SN:MWPT01000197.1   LN:2524072
skipping SAM header line:   @SQ SN:MWPT01000198.1   LN:2141569
skipping SAM header line:   @SQ SN:MWPT01000199.1   LN:2045508
skipping SAM header line:   @SQ SN:KV918282.1   LN:2192831
skipping SAM header line:   @SQ SN:KV918283.1   LN:3982359
skipping SAM header line:   @SQ SN:MWPT01000205.1   LN:1913558
skipping SAM header line:   @SQ SN:KV918284.1   LN:5938325
skipping SAM header line:   @SQ SN:MWPT01000213.1   LN:1819665
skipping SAM header line:   @SQ SN:KV918285.1   LN:3010866
skipping SAM header line:   @SQ SN:MWPT01000216.1   LN:1543109
skipping SAM header line:   @SQ SN:KV918286.1   LN:1541268
skipping SAM header line:   @SQ SN:MWPT01000219.1   LN:1527358
skipping SAM header line:   @SQ SN:MWPT01000220.1   LN:927761
skipping SAM header line:   @SQ SN:KV918287.1   LN:1495603
skipping SAM header line:   @SQ SN:MWPT01000225.1   LN:1391987
skipping SAM header line:   @SQ SN:MWPT01000226.1   LN:1267255
skipping SAM header line:   @SQ SN:MWPT01000227.1   LN:1262423
skipping SAM header line:   @SQ SN:MWPT01000228.1   LN:1255886
skipping SAM header line:   @SQ SN:KV918288.1   LN:2059602
skipping SAM header line:   @SQ SN:MWPT01000236.1   LN:1098465
skipping SAM header line:   @SQ SN:MWPT01000237.1   LN:1081217
skipping SAM header line:   @SQ SN:KV918289.1   LN:1222516
skipping SAM header line:   @SQ SN:MWPT01000241.1   LN:1057763
skipping SAM header line:   @SQ SN:KV918290.1   LN:2056098
skipping SAM header line:   @SQ SN:KV918291.1   LN:1857027
skipping SAM header line:   @SQ SN:KV918292.1   LN:1203224
skipping SAM header line:   @SQ SN:MWPT01000254.1   LN:865943
skipping SAM header line:   @SQ SN:KV918293.1   LN:904861
skipping SAM header line:   @SQ SN:MWPT01000257.1   LN:843307
skipping SAM header line:   @SQ SN:MWPT01000258.1   LN:872954
skipping SAM header line:   @SQ SN:KV918294.1   LN:1445946
skipping SAM header line:   @SQ SN:MWPT01000261.1   LN:815299
skipping SAM header line:   @SQ SN:MWPT01000262.1   LN:819735
skipping SAM header line:   @SQ SN:KV918295.1   LN:894170
skipping SAM header line:   @SQ SN:MWPT01000266.1   LN:593101
skipping SAM header line:   @SQ SN:MWPT01000267.1   LN:517245
skipping SAM header line:   @SQ SN:MWPT01000268.1   LN:422393
skipping SAM header line:   @SQ SN:KV918296.1   LN:374206
skipping SAM header line:   @SQ SN:MWPT01000271.1   LN:285735
skipping SAM header line:   @SQ SN:KV918297.1   LN:2638124
skipping SAM header line:   @SQ SN:MWPT01000132.1   LN:3069683
skipping SAM header line:   @SQ SN:KV918298.1   LN:6258228
skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
skipping SAM header line:   @SQ SN:KV918300.1   LN:4909813
skipping SAM header line:   @SQ SN:KV918301.1   LN:4886044
skipping SAM header line:   @SQ SN:MWPT01000292.1   LN:3102771
skipping SAM header line:   @SQ SN:KV918302.1   LN:4906456
skipping SAM header line:   @SQ SN:KV918303.1   LN:2044046
skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
skipping SAM header line:   @SQ SN:MWPT01000305.1   LN:2187399
skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
skipping SAM header line:   @SQ SN:KV918307.1   LN:2308754
skipping SAM header line:   @SQ SN:KV918308.1   LN:1938434
skipping SAM header line:   @SQ SN:MWPT01000320.1   LN:1317752
skipping SAM header line:   @SQ SN:KV918309.1   LN:1352802
skipping SAM header line:   @SQ SN:KV918310.1   LN:2226218
skipping SAM header line:   @SQ SN:MWPT01000328.1   LN:1052579
skipping SAM header line:   @SQ SN:KV918311.1   LN:923568
skipping SAM header line:   @SQ SN:KV918312.1   LN:1134795
skipping SAM header line:   @SQ SN:MWPT01000334.1   LN:885077
skipping SAM header line:   @SQ SN:MWPT01000335.1   LN:824456
skipping SAM header line:   @SQ SN:MWPT01000336.1   LN:765637
skipping SAM header line:   @SQ SN:KV918313.1   LN:584168
skipping SAM header line:   @SQ SN:KV918314.1   LN:944098
skipping SAM header line:   @SQ SN:KV918315.1   LN:808456
skipping SAM header line:   @SQ SN:MWPT01000343.1   LN:482633
skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
skipping SAM header line:   @SQ SN:KV918317.1   LN:2074599
skipping SAM header line:   @SQ SN:KV918318.1   LN:9119220
skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
skipping SAM header line:   @SQ SN:MWPT01000351.1   LN:4187197
skipping SAM header line:   @SQ SN:KV918319.1   LN:4367352
skipping SAM header line:   @SQ SN:KV918320.1   LN:4548939
skipping SAM header line:   @SQ SN:KV918321.1   LN:3696092
skipping SAM header line:   @SQ SN:KV918322.1   LN:3948338
skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
skipping SAM header line:   @SQ SN:KV918323.1   LN:4044222
skipping SAM header line:   @SQ SN:MWPT01000363.1   LN:2689329
skipping SAM header line:   @SQ SN:KV918324.1   LN:2791483
skipping SAM header line:   @SQ SN:KV918325.1   LN:2940093
skipping SAM header line:   @SQ SN:KV918326.1   LN:2068281
skipping SAM header line:   @SQ SN:KV918327.1   LN:2465851
skipping SAM header line:   @SQ SN:MWPT01000378.1   LN:748885
skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
skipping SAM header line:   @SQ SN:KV918330.1   LN:709582
skipping SAM header line:   @SQ SN:KV918331.1   LN:1455932
skipping SAM header line:   @SQ SN:KV918332.1   LN:5224090
skipping SAM header line:   @SQ SN:KV918333.1   LN:10098079
skipping SAM header line:   @SQ SN:KV918334.1   LN:10066667
skipping SAM header line:   @SQ SN:KV918335.1   LN:6231318
skipping SAM header line:   @SQ SN:MWPT01000396.1   LN:3199022
skipping SAM header line:   @SQ SN:MWPT01000398.1   LN:3334036
skipping SAM header line:   @SQ SN:MWPT01000403.1   LN:3473365
skipping SAM header line:   @SQ SN:MWPT01000404.1   LN:3037733
skipping SAM header line:   @SQ SN:MWPT01000405.1   LN:2721753
skipping SAM header line:   @SQ SN:KV918336.1   LN:2171808
skipping SAM header line:   @SQ SN:KV918337.1   LN:1620111
skipping SAM header line:   @SQ SN:KV918338.1   LN:1605531
skipping SAM header line:   @SQ SN:MWPT01000413.1   LN:509639
skipping SAM header line:   @SQ SN:KV918339.1   LN:166177
skipping SAM header line:   @SQ SN:KV918340.1   LN:592233
skipping SAM header line:   @SQ SN:MWPT01000012.1   LN:656707
skipping SAM header line:   @SQ SN:KV918341.1   LN:2281237
skipping SAM header line:   @SQ SN:MWPT01000416.1   LN:3228757
skipping SAM header line:   @SQ SN:MWPT01000417.1   LN:3070944
skipping SAM header line:   @SQ SN:MWPT01000418.1   LN:2999364
skipping SAM header line:   @SQ SN:KV918342.1   LN:2965468
skipping SAM header line:   @SQ SN:KV918343.1   LN:4001099
skipping SAM header line:   @SQ SN:KV918344.1   LN:2468544
skipping SAM header line:   @SQ SN:KV918345.1   LN:3799038
skipping SAM header line:   @SQ SN:MWPT01000430.1   LN:2027284
skipping SAM header line:   @SQ SN:KV918346.1   LN:2335779
skipping SAM header line:   @SQ SN:MWPT01000433.1   LN:1832700
skipping SAM header line:   @SQ SN:KV918347.1   LN:1755862
skipping SAM header line:   @SQ SN:KV918348.1   LN:1786188
skipping SAM header line:   @SQ SN:MWPT01000439.1   LN:1596044
skipping SAM header line:   @SQ SN:MWPT01000440.1   LN:1470869
skipping SAM header line:   @SQ SN:KV918349.1   LN:1124868
skipping SAM header line:   @SQ SN:MWPT01000446.1   LN:1358169
skipping SAM header line:   @SQ SN:MWPT01000447.1   LN:1303672
skipping SAM header line:   @SQ SN:MWPT01000448.1   LN:1292038
skipping SAM header line:   @SQ SN:KV918350.1   LN:2216547
skipping SAM header line:   @SQ SN:KV918351.1   LN:2144614
skipping SAM header line:   @SQ SN:KV918352.1   LN:2200068
skipping SAM header line:   @SQ SN:MWPT01000458.1   LN:1154801
skipping SAM header line:   @SQ SN:KV918353.1   LN:1249097
skipping SAM header line:   @SQ SN:MWPT01000461.1   LN:1054511
skipping SAM header line:   @SQ SN:MWPT01000462.1   LN:1029825
skipping SAM header line:   @SQ SN:KV918354.1   LN:1474778
skipping SAM header line:   @SQ SN:KV918355.1   LN:1882473
skipping SAM header line:   @SQ SN:KV918356.1   LN:1195088
skipping SAM header line:   @SQ SN:KV918357.1   LN:945790
skipping SAM header line:   @SQ SN:MWPT01000471.1   LN:901603
skipping SAM header line:   @SQ SN:MWPT01000472.1   LN:883242
skipping SAM header line:   @SQ SN:MWPT01000473.1   LN:863120
skipping SAM header line:   @SQ SN:KV918358.1   LN:906525
skipping SAM header line:   @SQ SN:KV918359.1   LN:1452728
skipping SAM header line:   @SQ SN:MWPT01000480.1   LN:748682
skipping SAM header line:   @SQ SN:KV918360.1   LN:659974
skipping SAM header line:   @SQ SN:KV918361.1   LN:466019
skipping SAM header line:   @SQ SN:MWPT01000013.1   LN:1300831
skipping SAM header line:   @SQ SN:MWPT01000131.1   LN:1971208
skipping SAM header line:   @SQ SN:KV918362.1   LN:2791541
skipping SAM header line:   @SQ SN:KV918363.1   LN:1907303
skipping SAM header line:   @SQ SN:MWPT01000397.1   LN:1723226
skipping SAM header line:   @SQ SN:MWPT01000410.1   LN:500894
skipping SAM header line:   @SQ SN:KV918364.1   LN:6892396
skipping SAM header line:   @SQ SN:KV918365.1   LN:7468933
skipping SAM header line:   @SQ SN:MWPT01000490.1   LN:3601090
skipping SAM header line:   @SQ SN:MWPT01000491.1   LN:2581635
skipping SAM header line:   @SQ SN:MWPT01000492.1   LN:2281164
skipping SAM header line:   @SQ SN:KV918366.1   LN:3576272
skipping SAM header line:   @SQ SN:KV918367.1   LN:3792723
skipping SAM header line:   @SQ SN:KV918368.1   LN:2247201
skipping SAM header line:   @SQ SN:KV918369.1   LN:2662616
skipping SAM header line:   @SQ SN:KV918370.1   LN:2530331
skipping SAM header line:   @SQ SN:MWPT01000510.1   LN:1983864
skipping SAM header line:   @SQ SN:KV918371.1   LN:1956835
skipping SAM header line:   @SQ SN:KV918372.1   LN:3086374
skipping SAM header line:   @SQ SN:KV918373.1   LN:3420601
skipping SAM header line:   @SQ SN:KV918374.1   LN:1975111
skipping SAM header line:   @SQ SN:MWPT01000522.1   LN:1408919
skipping SAM header line:   @SQ SN:KV918375.1   LN:2529433
skipping SAM header line:   @SQ SN:KV918376.1   LN:1290748
skipping SAM header line:   @SQ SN:KV918377.1   LN:2437656
skipping SAM header line:   @SQ SN:MWPT01000531.1   LN:1154204
skipping SAM header line:   @SQ SN:KV918378.1   LN:1139503
skipping SAM header line:   @SQ SN:MWPT01000536.1   LN:868008
skipping SAM header line:   @SQ SN:MWPT01000537.1   LN:771245
skipping SAM header line:   @SQ SN:KV918379.1   LN:1322005
skipping SAM header line:   @SQ SN:KV918380.1   LN:1966111
skipping SAM header line:   @SQ SN:MWPT01000546.1   LN:662674
skipping SAM header line:   @SQ SN:KV918381.1   LN:1109647
skipping SAM header line:   @SQ SN:KV918382.1   LN:871299
skipping SAM header line:   @SQ SN:MWPT01000551.1   LN:451986
skipping SAM header line:   @SQ SN:MWPT01000552.1   LN:323820
skipping SAM header line:   @SQ SN:MWPT01000553.1   LN:248130
skipping SAM header line:   @SQ SN:MWPT01000240.1   LN:21598
skipping SAM header line:   @SQ SN:KV918383.1   LN:3521928
skipping SAM header line:   @SQ SN:KV918384.1   LN:978841
skipping SAM header line:   @SQ SN:KV918385.1   LN:9025367
skipping SAM header line:   @SQ SN:MWPT01000562.1   LN:6788731
skipping SAM header line:   @SQ SN:MWPT01000563.1   LN:4429963
skipping SAM header line:   @SQ SN:KV918386.1   LN:3718566
skipping SAM header line:   @SQ SN:MWPT01000566.1   LN:2001120
skipping SAM header line:   @SQ SN:MWPT01000567.1   LN:1613306
skipping SAM header line:   @SQ SN:MWPT01000568.1   LN:1271813
skipping SAM header line:   @SQ SN:MWPT01000569.1   LN:1139655
skipping SAM header line:   @SQ SN:KV918387.1   LN:1748706
skipping SAM header line:   @SQ SN:KV918388.1   LN:1215097
skipping SAM header line:   @SQ SN:KV918389.1   LN:1703051
skipping SAM header line:   @SQ SN:MWPT01000577.1   LN:293636
skipping SAM header line:   @SQ SN:MWPT01000578.1   LN:295967
skipping SAM header line:   @SQ SN:MWPT01000072.1   LN:5034843
skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_GCCAAT_L001_R1.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_GCCAAT"
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4500000

Processed 4570127 lines in total
Total number of methylation call strings processed: 4570127

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   75497653

Total methylated C's in CpG context:    6598800
Total methylated C's in CHG context:    2357385
Total methylated C's in CHH context:    8320024

Total C to T conversions in CpG context:    7152028
Total C to T conversions in CHG context:    15918714
Total C to T conversions in CHH context:    35150702

C methylated in CpG context:    48.0%
C methylated in non-CpG context:    17.3%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->  kept
CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bam.txt contains data ->  kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_GCCAAT_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...


 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
skipping SAM header line:   @SQ SN:KV918245.1   LN:4832883
skipping SAM header line:   @SQ SN:KV918246.1   LN:4378960
skipping SAM header line:   @SQ SN:MWPT01000009.1   LN:3356639
skipping SAM header line:   @SQ SN:KV918247.1   LN:2355263
skipping SAM header line:   @SQ SN:KV918248.1   LN:3911507
skipping SAM header line:   @SQ SN:MWPT01000017.1   LN:2686679
skipping SAM header line:   @SQ SN:KV918249.1   LN:2829685
skipping SAM header line:   @SQ SN:KV918250.1   LN:3333291
skipping SAM header line:   @SQ SN:KV918251.1   LN:2850922
skipping SAM header line:   @SQ SN:KV918252.1   LN:5300508
skipping SAM header line:   @SQ SN:KV918253.1   LN:2652252
skipping SAM header line:   @SQ SN:KV918254.1   LN:3461433
skipping SAM header line:   @SQ SN:MWPT01000032.1   LN:1975305
skipping SAM header line:   @SQ SN:KV918255.1   LN:2606931
skipping SAM header line:   @SQ SN:MWPT01000041.1   LN:1717003
skipping SAM header line:   @SQ SN:KV918256.1   LN:2582953
skipping SAM header line:   @SQ SN:KV918257.1   LN:2738754
skipping SAM header line:   @SQ SN:MWPT01000052.1   LN:1062419
skipping SAM header line:   @SQ SN:KV918258.1   LN:1578002
skipping SAM header line:   @SQ SN:KV918259.1   LN:1347034
skipping SAM header line:   @SQ SN:KV918260.1   LN:684916
skipping SAM header line:   @SQ SN:MWPT01000061.1   LN:509886
skipping SAM header line:   @SQ SN:KV918261.1   LN:1120656
skipping SAM header line:   @SQ SN:MWPT01000067.1   LN:376046
skipping SAM header line:   @SQ SN:KV918262.1   LN:444482
skipping SAM header line:   @SQ SN:MWPT01000070.1   LN:357480
skipping SAM header line:   @SQ SN:MWPT01000071.1   LN:291238
skipping SAM header line:   @SQ SN:KV918263.1   LN:1230771
skipping SAM header line:   @SQ SN:MWPT01000527.1   LN:136883
skipping SAM header line:   @SQ SN:KV918264.1   LN:12680670
skipping SAM header line:   @SQ SN:KV918265.1   LN:2816827
skipping SAM header line:   @SQ SN:KV918266.1   LN:2977081
skipping SAM header line:   @SQ SN:MWPT01000137.1   LN:2796345
skipping SAM header line:   @SQ SN:MWPT01000138.1   LN:2693371
skipping SAM header line:   @SQ SN:MWPT01000139.1   LN:2365311
skipping SAM header line:   @SQ SN:MWPT01000140.1   LN:2238563
skipping SAM header line:   @SQ SN:MWPT01000141.1   LN:2207340
skipping SAM header line:   @SQ SN:KV918267.1   LN:2277360
skipping SAM header line:   @SQ SN:KV918268.1   LN:2822076
skipping SAM header line:   @SQ SN:KV918269.1   LN:3547160
skipping SAM header line:   @SQ SN:MWPT01000152.1   LN:1096595
skipping SAM header line:   @SQ SN:KV918270.1   LN:2145051
skipping SAM header line:   @SQ SN:KV918271.1   LN:1587102
skipping SAM header line:   @SQ SN:MWPT01000161.1   LN:1425844
skipping SAM header line:   @SQ SN:KV918272.1   LN:1907351
skipping SAM header line:   @SQ SN:MWPT01000166.1   LN:1422582
skipping SAM header line:   @SQ SN:KV918273.1   LN:1339065
skipping SAM header line:   @SQ SN:KV918274.1   LN:1546923
skipping SAM header line:   @SQ SN:KV918275.1   LN:1698010
skipping SAM header line:   @SQ SN:MWPT01000175.1   LN:1051837
skipping SAM header line:   @SQ SN:KV918276.1   LN:981967
skipping SAM header line:   @SQ SN:MWPT01000182.1   LN:448202
skipping SAM header line:   @SQ SN:KV918277.1   LN:917777
skipping SAM header line:   @SQ SN:MWPT01000185.1   LN:839050
skipping SAM header line:   @SQ SN:MWPT01000186.1   LN:724047
skipping SAM header line:   @SQ SN:MWPT01000187.1   LN:682532
skipping SAM header line:   @SQ SN:MWPT01000188.1   LN:392340
skipping SAM header line:   @SQ SN:MWPT01000189.1   LN:356808
skipping SAM header line:   @SQ SN:KV918278.1   LN:2436952
skipping SAM header line:   @SQ SN:KV918279.1   LN:385926
skipping SAM header line:   @SQ SN:KV918280.1   LN:1961913
skipping SAM header line:   @SQ SN:KV918281.1   LN:7786243
skipping SAM header line:   @SQ SN:MWPT01000194.1   LN:3534718
skipping SAM header line:   @SQ SN:MWPT01000195.1   LN:3254428
skipping SAM header line:   @SQ SN:MWPT01000196.1   LN:2889749
skipping SAM header line:   @SQ SN:MWPT01000197.1   LN:2524072
skipping SAM header line:   @SQ SN:MWPT01000198.1   LN:2141569
skipping SAM header line:   @SQ SN:MWPT01000199.1   LN:2045508
skipping SAM header line:   @SQ SN:KV918282.1   LN:2192831
skipping SAM header line:   @SQ SN:KV918283.1   LN:3982359
skipping SAM header line:   @SQ SN:MWPT01000205.1   LN:1913558
skipping SAM header line:   @SQ SN:KV918284.1   LN:5938325
skipping SAM header line:   @SQ SN:MWPT01000213.1   LN:1819665
skipping SAM header line:   @SQ SN:KV918285.1   LN:3010866
skipping SAM header line:   @SQ SN:MWPT01000216.1   LN:1543109
skipping SAM header line:   @SQ SN:KV918286.1   LN:1541268
skipping SAM header line:   @SQ SN:MWPT01000219.1   LN:1527358
skipping SAM header line:   @SQ SN:MWPT01000220.1   LN:927761
skipping SAM header line:   @SQ SN:KV918287.1   LN:1495603
skipping SAM header line:   @SQ SN:MWPT01000225.1   LN:1391987
skipping SAM header line:   @SQ SN:MWPT01000226.1   LN:1267255
skipping SAM header line:   @SQ SN:MWPT01000227.1   LN:1262423
skipping SAM header line:   @SQ SN:MWPT01000228.1   LN:1255886
skipping SAM header line:   @SQ SN:KV918288.1   LN:2059602
skipping SAM header line:   @SQ SN:MWPT01000236.1   LN:1098465
skipping SAM header line:   @SQ SN:MWPT01000237.1   LN:1081217
skipping SAM header line:   @SQ SN:KV918289.1   LN:1222516
skipping SAM header line:   @SQ SN:MWPT01000241.1   LN:1057763
skipping SAM header line:   @SQ SN:KV918290.1   LN:2056098
skipping SAM header line:   @SQ SN:KV918291.1   LN:1857027
skipping SAM header line:   @SQ SN:KV918292.1   LN:1203224
skipping SAM header line:   @SQ SN:MWPT01000254.1   LN:865943
skipping SAM header line:   @SQ SN:KV918293.1   LN:904861
skipping SAM header line:   @SQ SN:MWPT01000257.1   LN:843307
skipping SAM header line:   @SQ SN:MWPT01000258.1   LN:872954
skipping SAM header line:   @SQ SN:KV918294.1   LN:1445946
skipping SAM header line:   @SQ SN:MWPT01000261.1   LN:815299
skipping SAM header line:   @SQ SN:MWPT01000262.1   LN:819735
skipping SAM header line:   @SQ SN:KV918295.1   LN:894170
skipping SAM header line:   @SQ SN:MWPT01000266.1   LN:593101
skipping SAM header line:   @SQ SN:MWPT01000267.1   LN:517245
skipping SAM header line:   @SQ SN:MWPT01000268.1   LN:422393
skipping SAM header line:   @SQ SN:KV918296.1   LN:374206
skipping SAM header line:   @SQ SN:MWPT01000271.1   LN:285735
skipping SAM header line:   @SQ SN:KV918297.1   LN:2638124
skipping SAM header line:   @SQ SN:MWPT01000132.1   LN:3069683
skipping SAM header line:   @SQ SN:KV918298.1   LN:6258228
skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
skipping SAM header line:   @SQ SN:KV918300.1   LN:4909813
skipping SAM header line:   @SQ SN:KV918301.1   LN:4886044
skipping SAM header line:   @SQ SN:MWPT01000292.1   LN:3102771
skipping SAM header line:   @SQ SN:KV918302.1   LN:4906456
skipping SAM header line:   @SQ SN:KV918303.1   LN:2044046
skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
skipping SAM header line:   @SQ SN:MWPT01000305.1   LN:2187399
skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
skipping SAM header line:   @SQ SN:KV918307.1   LN:2308754
skipping SAM header line:   @SQ SN:KV918308.1   LN:1938434
skipping SAM header line:   @SQ SN:MWPT01000320.1   LN:1317752
skipping SAM header line:   @SQ SN:KV918309.1   LN:1352802
skipping SAM header line:   @SQ SN:KV918310.1   LN:2226218
skipping SAM header line:   @SQ SN:MWPT01000328.1   LN:1052579
skipping SAM header line:   @SQ SN:KV918311.1   LN:923568
skipping SAM header line:   @SQ SN:KV918312.1   LN:1134795
skipping SAM header line:   @SQ SN:MWPT01000334.1   LN:885077
skipping SAM header line:   @SQ SN:MWPT01000335.1   LN:824456
skipping SAM header line:   @SQ SN:MWPT01000336.1   LN:765637
skipping SAM header line:   @SQ SN:KV918313.1   LN:584168
skipping SAM header line:   @SQ SN:KV918314.1   LN:944098
skipping SAM header line:   @SQ SN:KV918315.1   LN:808456
skipping SAM header line:   @SQ SN:MWPT01000343.1   LN:482633
skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
skipping SAM header line:   @SQ SN:KV918317.1   LN:2074599
skipping SAM header line:   @SQ SN:KV918318.1   LN:9119220
skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
skipping SAM header line:   @SQ SN:MWPT01000351.1   LN:4187197
skipping SAM header line:   @SQ SN:KV918319.1   LN:4367352
skipping SAM header line:   @SQ SN:KV918320.1   LN:4548939
skipping SAM header line:   @SQ SN:KV918321.1   LN:3696092
skipping SAM header line:   @SQ SN:KV918322.1   LN:3948338
skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
skipping SAM header line:   @SQ SN:KV918323.1   LN:4044222
skipping SAM header line:   @SQ SN:MWPT01000363.1   LN:2689329
skipping SAM header line:   @SQ SN:KV918324.1   LN:2791483
skipping SAM header line:   @SQ SN:KV918325.1   LN:2940093
skipping SAM header line:   @SQ SN:KV918326.1   LN:2068281
skipping SAM header line:   @SQ SN:KV918327.1   LN:2465851
skipping SAM header line:   @SQ SN:MWPT01000378.1   LN:748885
skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
skipping SAM header line:   @SQ SN:KV918330.1   LN:709582
skipping SAM header line:   @SQ SN:KV918331.1   LN:1455932
skipping SAM header line:   @SQ SN:KV918332.1   LN:5224090
skipping SAM header line:   @SQ SN:KV918333.1   LN:10098079
skipping SAM header line:   @SQ SN:KV918334.1   LN:10066667
skipping SAM header line:   @SQ SN:KV918335.1   LN:6231318
skipping SAM header line:   @SQ SN:MWPT01000396.1   LN:3199022
skipping SAM header line:   @SQ SN:MWPT01000398.1   LN:3334036
skipping SAM header line:   @SQ SN:MWPT01000403.1   LN:3473365
skipping SAM header line:   @SQ SN:MWPT01000404.1   LN:3037733
skipping SAM header line:   @SQ SN:MWPT01000405.1   LN:2721753
skipping SAM header line:   @SQ SN:KV918336.1   LN:2171808
skipping SAM header line:   @SQ SN:KV918337.1   LN:1620111
skipping SAM header line:   @SQ SN:KV918338.1   LN:1605531
skipping SAM header line:   @SQ SN:MWPT01000413.1   LN:509639
skipping SAM header line:   @SQ SN:KV918339.1   LN:166177
skipping SAM header line:   @SQ SN:KV918340.1   LN:592233
skipping SAM header line:   @SQ SN:MWPT01000012.1   LN:656707
skipping SAM header line:   @SQ SN:KV918341.1   LN:2281237
skipping SAM header line:   @SQ SN:MWPT01000416.1   LN:3228757
skipping SAM header line:   @SQ SN:MWPT01000417.1   LN:3070944
skipping SAM header line:   @SQ SN:MWPT01000418.1   LN:2999364
skipping SAM header line:   @SQ SN:KV918342.1   LN:2965468
skipping SAM header line:   @SQ SN:KV918343.1   LN:4001099
skipping SAM header line:   @SQ SN:KV918344.1   LN:2468544
skipping SAM header line:   @SQ SN:KV918345.1   LN:3799038
skipping SAM header line:   @SQ SN:MWPT01000430.1   LN:2027284
skipping SAM header line:   @SQ SN:KV918346.1   LN:2335779
skipping SAM header line:   @SQ SN:MWPT01000433.1   LN:1832700
skipping SAM header line:   @SQ SN:KV918347.1   LN:1755862
skipping SAM header line:   @SQ SN:KV918348.1   LN:1786188
skipping SAM header line:   @SQ SN:MWPT01000439.1   LN:1596044
skipping SAM header line:   @SQ SN:MWPT01000440.1   LN:1470869
skipping SAM header line:   @SQ SN:KV918349.1   LN:1124868
skipping SAM header line:   @SQ SN:MWPT01000446.1   LN:1358169
skipping SAM header line:   @SQ SN:MWPT01000447.1   LN:1303672
skipping SAM header line:   @SQ SN:MWPT01000448.1   LN:1292038
skipping SAM header line:   @SQ SN:KV918350.1   LN:2216547
skipping SAM header line:   @SQ SN:KV918351.1   LN:2144614
skipping SAM header line:   @SQ SN:KV918352.1   LN:2200068
skipping SAM header line:   @SQ SN:MWPT01000458.1   LN:1154801
skipping SAM header line:   @SQ SN:KV918353.1   LN:1249097
skipping SAM header line:   @SQ SN:MWPT01000461.1   LN:1054511
skipping SAM header line:   @SQ SN:MWPT01000462.1   LN:1029825
skipping SAM header line:   @SQ SN:KV918354.1   LN:1474778
skipping SAM header line:   @SQ SN:KV918355.1   LN:1882473
skipping SAM header line:   @SQ SN:KV918356.1   LN:1195088
skipping SAM header line:   @SQ SN:KV918357.1   LN:945790
skipping SAM header line:   @SQ SN:MWPT01000471.1   LN:901603
skipping SAM header line:   @SQ SN:MWPT01000472.1   LN:883242
skipping SAM header line:   @SQ SN:MWPT01000473.1   LN:863120
skipping SAM header line:   @SQ SN:KV918358.1   LN:906525
skipping SAM header line:   @SQ SN:KV918359.1   LN:1452728
skipping SAM header line:   @SQ SN:MWPT01000480.1   LN:748682
skipping SAM header line:   @SQ SN:KV918360.1   LN:659974
skipping SAM header line:   @SQ SN:KV918361.1   LN:466019
skipping SAM header line:   @SQ SN:MWPT01000013.1   LN:1300831
skipping SAM header line:   @SQ SN:MWPT01000131.1   LN:1971208
skipping SAM header line:   @SQ SN:KV918362.1   LN:2791541
skipping SAM header line:   @SQ SN:KV918363.1   LN:1907303
skipping SAM header line:   @SQ SN:MWPT01000397.1   LN:1723226
skipping SAM header line:   @SQ SN:MWPT01000410.1   LN:500894
skipping SAM header line:   @SQ SN:KV918364.1   LN:6892396
skipping SAM header line:   @SQ SN:KV918365.1   LN:7468933
skipping SAM header line:   @SQ SN:MWPT01000490.1   LN:3601090
skipping SAM header line:   @SQ SN:MWPT01000491.1   LN:2581635
skipping SAM header line:   @SQ SN:MWPT01000492.1   LN:2281164
skipping SAM header line:   @SQ SN:KV918366.1   LN:3576272
skipping SAM header line:   @SQ SN:KV918367.1   LN:3792723
skipping SAM header line:   @SQ SN:KV918368.1   LN:2247201
skipping SAM header line:   @SQ SN:KV918369.1   LN:2662616
skipping SAM header line:   @SQ SN:KV918370.1   LN:2530331
skipping SAM header line:   @SQ SN:MWPT01000510.1   LN:1983864
skipping SAM header line:   @SQ SN:KV918371.1   LN:1956835
skipping SAM header line:   @SQ SN:KV918372.1   LN:3086374
skipping SAM header line:   @SQ SN:KV918373.1   LN:3420601
skipping SAM header line:   @SQ SN:KV918374.1   LN:1975111
skipping SAM header line:   @SQ SN:MWPT01000522.1   LN:1408919
skipping SAM header line:   @SQ SN:KV918375.1   LN:2529433
skipping SAM header line:   @SQ SN:KV918376.1   LN:1290748
skipping SAM header line:   @SQ SN:KV918377.1   LN:2437656
skipping SAM header line:   @SQ SN:MWPT01000531.1   LN:1154204
skipping SAM header line:   @SQ SN:KV918378.1   LN:1139503
skipping SAM header line:   @SQ SN:MWPT01000536.1   LN:868008
skipping SAM header line:   @SQ SN:MWPT01000537.1   LN:771245
skipping SAM header line:   @SQ SN:KV918379.1   LN:1322005
skipping SAM header line:   @SQ SN:KV918380.1   LN:1966111
skipping SAM header line:   @SQ SN:MWPT01000546.1   LN:662674
skipping SAM header line:   @SQ SN:KV918381.1   LN:1109647
skipping SAM header line:   @SQ SN:KV918382.1   LN:871299
skipping SAM header line:   @SQ SN:MWPT01000551.1   LN:451986
skipping SAM header line:   @SQ SN:MWPT01000552.1   LN:323820
skipping SAM header line:   @SQ SN:MWPT01000553.1   LN:248130
skipping SAM header line:   @SQ SN:MWPT01000240.1   LN:21598
skipping SAM header line:   @SQ SN:KV918383.1   LN:3521928
skipping SAM header line:   @SQ SN:KV918384.1   LN:978841
skipping SAM header line:   @SQ SN:KV918385.1   LN:9025367
skipping SAM header line:   @SQ SN:MWPT01000562.1   LN:6788731
skipping SAM header line:   @SQ SN:MWPT01000563.1   LN:4429963
skipping SAM header line:   @SQ SN:KV918386.1   LN:3718566
skipping SAM header line:   @SQ SN:MWPT01000566.1   LN:2001120
skipping SAM header line:   @SQ SN:MWPT01000567.1   LN:1613306
skipping SAM header line:   @SQ SN:MWPT01000568.1   LN:1271813
skipping SAM header line:   @SQ SN:MWPT01000569.1   LN:1139655
skipping SAM header line:   @SQ SN:KV918387.1   LN:1748706
skipping SAM header line:   @SQ SN:KV918388.1   LN:1215097
skipping SAM header line:   @SQ SN:KV918389.1   LN:1703051
skipping SAM header line:   @SQ SN:MWPT01000577.1   LN:293636
skipping SAM header line:   @SQ SN:MWPT01000578.1   LN:295967
skipping SAM header line:   @SQ SN:MWPT01000072.1   LN:5034843
skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_TGACCA_L001_R1_001.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_TGACCA"
Processed lines: 500000

Processed 623273 lines in total
Total number of methylation call strings processed: 623273

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   10412368

Total methylated C's in CpG context:    2215432
Total methylated C's in CHG context:    1428445
Total methylated C's in CHH context:    3781284

Total C to T conversions in CpG context:    261842
Total C to T conversions in CHG context:    1215969
Total C to T conversions in CHH context:    1509396

C methylated in CpG context:    89.4%
C methylated in non-CpG context:    65.7%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->  kept
CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->    kept
CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->    kept
CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->  kept
Non_CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->  kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->    kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt contains data ->    kept
Non_CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bam.txt contains data ->  kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_TGACCA_L001_R1_001_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...


 *** Bismark methylation extractor version v0.16.3 ***

Trying to determine the type of mapping from the SAM header line of file hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bam
Treating file(s) as single-end data (as extracted from @PG line)

Setting core usage to single-threaded (default). Consider using --multicore <int> to speed up the extraction process.

Summarising Bismark methylation extractor parameters:
===============================================================
Bismark single-end SAM format specified (default)
Number of cores to be used: 1
Merge CHG and CHH context to non-CpG context specified
Output will be written to the current directory ('/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction')


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>

Writing out an additional coverage file (ending in zero.cov) with 0-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Using a cutoff of 1 read(s) to report cytosine positions
Reporting and sorting cytosine methylation information in CpG context only (default)
The bedGraph UNIX sort command will use the following memory setting:   '2G'. Temporary directory used for sorting is the output directory

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt

Writing result file containing methylation information for C in any other context from the original top strand to Non_CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original top strand to Non_CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the complementary to original bottom strand to Non_CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt
Writing result file containing methylation information for C in any other context from the original bottom strand to Non_CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bam.txt

Now reading in Bismark result file hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bam
skipping SAM header line:   @HD VN:1.0  SO:unsorted
skipping SAM header line:   @SQ SN:KV918244.1   LN:5562293
skipping SAM header line:   @SQ SN:KV918245.1   LN:4832883
skipping SAM header line:   @SQ SN:KV918246.1   LN:4378960
skipping SAM header line:   @SQ SN:MWPT01000009.1   LN:3356639
skipping SAM header line:   @SQ SN:KV918247.1   LN:2355263
skipping SAM header line:   @SQ SN:KV918248.1   LN:3911507
skipping SAM header line:   @SQ SN:MWPT01000017.1   LN:2686679
skipping SAM header line:   @SQ SN:KV918249.1   LN:2829685
skipping SAM header line:   @SQ SN:KV918250.1   LN:3333291
skipping SAM header line:   @SQ SN:KV918251.1   LN:2850922
skipping SAM header line:   @SQ SN:KV918252.1   LN:5300508
skipping SAM header line:   @SQ SN:KV918253.1   LN:2652252
skipping SAM header line:   @SQ SN:KV918254.1   LN:3461433
skipping SAM header line:   @SQ SN:MWPT01000032.1   LN:1975305
skipping SAM header line:   @SQ SN:KV918255.1   LN:2606931
skipping SAM header line:   @SQ SN:MWPT01000041.1   LN:1717003
skipping SAM header line:   @SQ SN:KV918256.1   LN:2582953
skipping SAM header line:   @SQ SN:KV918257.1   LN:2738754
skipping SAM header line:   @SQ SN:MWPT01000052.1   LN:1062419
skipping SAM header line:   @SQ SN:KV918258.1   LN:1578002
skipping SAM header line:   @SQ SN:KV918259.1   LN:1347034
skipping SAM header line:   @SQ SN:KV918260.1   LN:684916
skipping SAM header line:   @SQ SN:MWPT01000061.1   LN:509886
skipping SAM header line:   @SQ SN:KV918261.1   LN:1120656
skipping SAM header line:   @SQ SN:MWPT01000067.1   LN:376046
skipping SAM header line:   @SQ SN:KV918262.1   LN:444482
skipping SAM header line:   @SQ SN:MWPT01000070.1   LN:357480
skipping SAM header line:   @SQ SN:MWPT01000071.1   LN:291238
skipping SAM header line:   @SQ SN:KV918263.1   LN:1230771
skipping SAM header line:   @SQ SN:MWPT01000527.1   LN:136883
skipping SAM header line:   @SQ SN:KV918264.1   LN:12680670
skipping SAM header line:   @SQ SN:KV918265.1   LN:2816827
skipping SAM header line:   @SQ SN:KV918266.1   LN:2977081
skipping SAM header line:   @SQ SN:MWPT01000137.1   LN:2796345
skipping SAM header line:   @SQ SN:MWPT01000138.1   LN:2693371
skipping SAM header line:   @SQ SN:MWPT01000139.1   LN:2365311
skipping SAM header line:   @SQ SN:MWPT01000140.1   LN:2238563
skipping SAM header line:   @SQ SN:MWPT01000141.1   LN:2207340
skipping SAM header line:   @SQ SN:KV918267.1   LN:2277360
skipping SAM header line:   @SQ SN:KV918268.1   LN:2822076
skipping SAM header line:   @SQ SN:KV918269.1   LN:3547160
skipping SAM header line:   @SQ SN:MWPT01000152.1   LN:1096595
skipping SAM header line:   @SQ SN:KV918270.1   LN:2145051
skipping SAM header line:   @SQ SN:KV918271.1   LN:1587102
skipping SAM header line:   @SQ SN:MWPT01000161.1   LN:1425844
skipping SAM header line:   @SQ SN:KV918272.1   LN:1907351
skipping SAM header line:   @SQ SN:MWPT01000166.1   LN:1422582
skipping SAM header line:   @SQ SN:KV918273.1   LN:1339065
skipping SAM header line:   @SQ SN:KV918274.1   LN:1546923
skipping SAM header line:   @SQ SN:KV918275.1   LN:1698010
skipping SAM header line:   @SQ SN:MWPT01000175.1   LN:1051837
skipping SAM header line:   @SQ SN:KV918276.1   LN:981967
skipping SAM header line:   @SQ SN:MWPT01000182.1   LN:448202
skipping SAM header line:   @SQ SN:KV918277.1   LN:917777
skipping SAM header line:   @SQ SN:MWPT01000185.1   LN:839050
skipping SAM header line:   @SQ SN:MWPT01000186.1   LN:724047
skipping SAM header line:   @SQ SN:MWPT01000187.1   LN:682532
skipping SAM header line:   @SQ SN:MWPT01000188.1   LN:392340
skipping SAM header line:   @SQ SN:MWPT01000189.1   LN:356808
skipping SAM header line:   @SQ SN:KV918278.1   LN:2436952
skipping SAM header line:   @SQ SN:KV918279.1   LN:385926
skipping SAM header line:   @SQ SN:KV918280.1   LN:1961913
skipping SAM header line:   @SQ SN:KV918281.1   LN:7786243
skipping SAM header line:   @SQ SN:MWPT01000194.1   LN:3534718
skipping SAM header line:   @SQ SN:MWPT01000195.1   LN:3254428
skipping SAM header line:   @SQ SN:MWPT01000196.1   LN:2889749
skipping SAM header line:   @SQ SN:MWPT01000197.1   LN:2524072
skipping SAM header line:   @SQ SN:MWPT01000198.1   LN:2141569
skipping SAM header line:   @SQ SN:MWPT01000199.1   LN:2045508
skipping SAM header line:   @SQ SN:KV918282.1   LN:2192831
skipping SAM header line:   @SQ SN:KV918283.1   LN:3982359
skipping SAM header line:   @SQ SN:MWPT01000205.1   LN:1913558
skipping SAM header line:   @SQ SN:KV918284.1   LN:5938325
skipping SAM header line:   @SQ SN:MWPT01000213.1   LN:1819665
skipping SAM header line:   @SQ SN:KV918285.1   LN:3010866
skipping SAM header line:   @SQ SN:MWPT01000216.1   LN:1543109
skipping SAM header line:   @SQ SN:KV918286.1   LN:1541268
skipping SAM header line:   @SQ SN:MWPT01000219.1   LN:1527358
skipping SAM header line:   @SQ SN:MWPT01000220.1   LN:927761
skipping SAM header line:   @SQ SN:KV918287.1   LN:1495603
skipping SAM header line:   @SQ SN:MWPT01000225.1   LN:1391987
skipping SAM header line:   @SQ SN:MWPT01000226.1   LN:1267255
skipping SAM header line:   @SQ SN:MWPT01000227.1   LN:1262423
skipping SAM header line:   @SQ SN:MWPT01000228.1   LN:1255886
skipping SAM header line:   @SQ SN:KV918288.1   LN:2059602
skipping SAM header line:   @SQ SN:MWPT01000236.1   LN:1098465
skipping SAM header line:   @SQ SN:MWPT01000237.1   LN:1081217
skipping SAM header line:   @SQ SN:KV918289.1   LN:1222516
skipping SAM header line:   @SQ SN:MWPT01000241.1   LN:1057763
skipping SAM header line:   @SQ SN:KV918290.1   LN:2056098
skipping SAM header line:   @SQ SN:KV918291.1   LN:1857027
skipping SAM header line:   @SQ SN:KV918292.1   LN:1203224
skipping SAM header line:   @SQ SN:MWPT01000254.1   LN:865943
skipping SAM header line:   @SQ SN:KV918293.1   LN:904861
skipping SAM header line:   @SQ SN:MWPT01000257.1   LN:843307
skipping SAM header line:   @SQ SN:MWPT01000258.1   LN:872954
skipping SAM header line:   @SQ SN:KV918294.1   LN:1445946
skipping SAM header line:   @SQ SN:MWPT01000261.1   LN:815299
skipping SAM header line:   @SQ SN:MWPT01000262.1   LN:819735
skipping SAM header line:   @SQ SN:KV918295.1   LN:894170
skipping SAM header line:   @SQ SN:MWPT01000266.1   LN:593101
skipping SAM header line:   @SQ SN:MWPT01000267.1   LN:517245
skipping SAM header line:   @SQ SN:MWPT01000268.1   LN:422393
skipping SAM header line:   @SQ SN:KV918296.1   LN:374206
skipping SAM header line:   @SQ SN:MWPT01000271.1   LN:285735
skipping SAM header line:   @SQ SN:KV918297.1   LN:2638124
skipping SAM header line:   @SQ SN:MWPT01000132.1   LN:3069683
skipping SAM header line:   @SQ SN:KV918298.1   LN:6258228
skipping SAM header line:   @SQ SN:KV918299.1   LN:4762230
skipping SAM header line:   @SQ SN:KV918300.1   LN:4909813
skipping SAM header line:   @SQ SN:KV918301.1   LN:4886044
skipping SAM header line:   @SQ SN:MWPT01000292.1   LN:3102771
skipping SAM header line:   @SQ SN:KV918302.1   LN:4906456
skipping SAM header line:   @SQ SN:KV918303.1   LN:2044046
skipping SAM header line:   @SQ SN:MWPT01000301.1   LN:2550412
skipping SAM header line:   @SQ SN:KV918304.1   LN:2515771
skipping SAM header line:   @SQ SN:MWPT01000305.1   LN:2187399
skipping SAM header line:   @SQ SN:KV918305.1   LN:5410003
skipping SAM header line:   @SQ SN:KV918306.1   LN:2272750
skipping SAM header line:   @SQ SN:MWPT01000313.1   LN:1775320
skipping SAM header line:   @SQ SN:MWPT01000314.1   LN:1603798
skipping SAM header line:   @SQ SN:KV918307.1   LN:2308754
skipping SAM header line:   @SQ SN:KV918308.1   LN:1938434
skipping SAM header line:   @SQ SN:MWPT01000320.1   LN:1317752
skipping SAM header line:   @SQ SN:KV918309.1   LN:1352802
skipping SAM header line:   @SQ SN:KV918310.1   LN:2226218
skipping SAM header line:   @SQ SN:MWPT01000328.1   LN:1052579
skipping SAM header line:   @SQ SN:KV918311.1   LN:923568
skipping SAM header line:   @SQ SN:KV918312.1   LN:1134795
skipping SAM header line:   @SQ SN:MWPT01000334.1   LN:885077
skipping SAM header line:   @SQ SN:MWPT01000335.1   LN:824456
skipping SAM header line:   @SQ SN:MWPT01000336.1   LN:765637
skipping SAM header line:   @SQ SN:KV918313.1   LN:584168
skipping SAM header line:   @SQ SN:KV918314.1   LN:944098
skipping SAM header line:   @SQ SN:KV918315.1   LN:808456
skipping SAM header line:   @SQ SN:MWPT01000343.1   LN:482633
skipping SAM header line:   @SQ SN:KV918316.1   LN:643206
skipping SAM header line:   @SQ SN:MWPT01000421.1   LN:484002
skipping SAM header line:   @SQ SN:MWPT01000532.1   LN:470776
skipping SAM header line:   @SQ SN:KV918317.1   LN:2074599
skipping SAM header line:   @SQ SN:KV918318.1   LN:9119220
skipping SAM header line:   @SQ SN:MWPT01000350.1   LN:4491256
skipping SAM header line:   @SQ SN:MWPT01000351.1   LN:4187197
skipping SAM header line:   @SQ SN:KV918319.1   LN:4367352
skipping SAM header line:   @SQ SN:KV918320.1   LN:4548939
skipping SAM header line:   @SQ SN:KV918321.1   LN:3696092
skipping SAM header line:   @SQ SN:KV918322.1   LN:3948338
skipping SAM header line:   @SQ SN:MWPT01000360.1   LN:2892682
skipping SAM header line:   @SQ SN:KV918323.1   LN:4044222
skipping SAM header line:   @SQ SN:MWPT01000363.1   LN:2689329
skipping SAM header line:   @SQ SN:KV918324.1   LN:2791483
skipping SAM header line:   @SQ SN:KV918325.1   LN:2940093
skipping SAM header line:   @SQ SN:KV918326.1   LN:2068281
skipping SAM header line:   @SQ SN:KV918327.1   LN:2465851
skipping SAM header line:   @SQ SN:MWPT01000378.1   LN:748885
skipping SAM header line:   @SQ SN:MWPT01000379.1   LN:589915
skipping SAM header line:   @SQ SN:MWPT01000380.1   LN:554808
skipping SAM header line:   @SQ SN:MWPT01000381.1   LN:489263
skipping SAM header line:   @SQ SN:KV918328.1   LN:464725
skipping SAM header line:   @SQ SN:KV918329.1   LN:469357
skipping SAM header line:   @SQ SN:MWPT01000386.1   LN:391304
skipping SAM header line:   @SQ SN:MWPT01000387.1   LN:243720
skipping SAM header line:   @SQ SN:KV918330.1   LN:709582
skipping SAM header line:   @SQ SN:KV918331.1   LN:1455932
skipping SAM header line:   @SQ SN:KV918332.1   LN:5224090
skipping SAM header line:   @SQ SN:KV918333.1   LN:10098079
skipping SAM header line:   @SQ SN:KV918334.1   LN:10066667
skipping SAM header line:   @SQ SN:KV918335.1   LN:6231318
skipping SAM header line:   @SQ SN:MWPT01000396.1   LN:3199022
skipping SAM header line:   @SQ SN:MWPT01000398.1   LN:3334036
skipping SAM header line:   @SQ SN:MWPT01000403.1   LN:3473365
skipping SAM header line:   @SQ SN:MWPT01000404.1   LN:3037733
skipping SAM header line:   @SQ SN:MWPT01000405.1   LN:2721753
skipping SAM header line:   @SQ SN:KV918336.1   LN:2171808
skipping SAM header line:   @SQ SN:KV918337.1   LN:1620111
skipping SAM header line:   @SQ SN:KV918338.1   LN:1605531
skipping SAM header line:   @SQ SN:MWPT01000413.1   LN:509639
skipping SAM header line:   @SQ SN:KV918339.1   LN:166177
skipping SAM header line:   @SQ SN:KV918340.1   LN:592233
skipping SAM header line:   @SQ SN:MWPT01000012.1   LN:656707
skipping SAM header line:   @SQ SN:KV918341.1   LN:2281237
skipping SAM header line:   @SQ SN:MWPT01000416.1   LN:3228757
skipping SAM header line:   @SQ SN:MWPT01000417.1   LN:3070944
skipping SAM header line:   @SQ SN:MWPT01000418.1   LN:2999364
skipping SAM header line:   @SQ SN:KV918342.1   LN:2965468
skipping SAM header line:   @SQ SN:KV918343.1   LN:4001099
skipping SAM header line:   @SQ SN:KV918344.1   LN:2468544
skipping SAM header line:   @SQ SN:KV918345.1   LN:3799038
skipping SAM header line:   @SQ SN:MWPT01000430.1   LN:2027284
skipping SAM header line:   @SQ SN:KV918346.1   LN:2335779
skipping SAM header line:   @SQ SN:MWPT01000433.1   LN:1832700
skipping SAM header line:   @SQ SN:KV918347.1   LN:1755862
skipping SAM header line:   @SQ SN:KV918348.1   LN:1786188
skipping SAM header line:   @SQ SN:MWPT01000439.1   LN:1596044
skipping SAM header line:   @SQ SN:MWPT01000440.1   LN:1470869
skipping SAM header line:   @SQ SN:KV918349.1   LN:1124868
skipping SAM header line:   @SQ SN:MWPT01000446.1   LN:1358169
skipping SAM header line:   @SQ SN:MWPT01000447.1   LN:1303672
skipping SAM header line:   @SQ SN:MWPT01000448.1   LN:1292038
skipping SAM header line:   @SQ SN:KV918350.1   LN:2216547
skipping SAM header line:   @SQ SN:KV918351.1   LN:2144614
skipping SAM header line:   @SQ SN:KV918352.1   LN:2200068
skipping SAM header line:   @SQ SN:MWPT01000458.1   LN:1154801
skipping SAM header line:   @SQ SN:KV918353.1   LN:1249097
skipping SAM header line:   @SQ SN:MWPT01000461.1   LN:1054511
skipping SAM header line:   @SQ SN:MWPT01000462.1   LN:1029825
skipping SAM header line:   @SQ SN:KV918354.1   LN:1474778
skipping SAM header line:   @SQ SN:KV918355.1   LN:1882473
skipping SAM header line:   @SQ SN:KV918356.1   LN:1195088
skipping SAM header line:   @SQ SN:KV918357.1   LN:945790
skipping SAM header line:   @SQ SN:MWPT01000471.1   LN:901603
skipping SAM header line:   @SQ SN:MWPT01000472.1   LN:883242
skipping SAM header line:   @SQ SN:MWPT01000473.1   LN:863120
skipping SAM header line:   @SQ SN:KV918358.1   LN:906525
skipping SAM header line:   @SQ SN:KV918359.1   LN:1452728
skipping SAM header line:   @SQ SN:MWPT01000480.1   LN:748682
skipping SAM header line:   @SQ SN:KV918360.1   LN:659974
skipping SAM header line:   @SQ SN:KV918361.1   LN:466019
skipping SAM header line:   @SQ SN:MWPT01000013.1   LN:1300831
skipping SAM header line:   @SQ SN:MWPT01000131.1   LN:1971208
skipping SAM header line:   @SQ SN:KV918362.1   LN:2791541
skipping SAM header line:   @SQ SN:KV918363.1   LN:1907303
skipping SAM header line:   @SQ SN:MWPT01000397.1   LN:1723226
skipping SAM header line:   @SQ SN:MWPT01000410.1   LN:500894
skipping SAM header line:   @SQ SN:KV918364.1   LN:6892396
skipping SAM header line:   @SQ SN:KV918365.1   LN:7468933
skipping SAM header line:   @SQ SN:MWPT01000490.1   LN:3601090
skipping SAM header line:   @SQ SN:MWPT01000491.1   LN:2581635
skipping SAM header line:   @SQ SN:MWPT01000492.1   LN:2281164
skipping SAM header line:   @SQ SN:KV918366.1   LN:3576272
skipping SAM header line:   @SQ SN:KV918367.1   LN:3792723
skipping SAM header line:   @SQ SN:KV918368.1   LN:2247201
skipping SAM header line:   @SQ SN:KV918369.1   LN:2662616
skipping SAM header line:   @SQ SN:KV918370.1   LN:2530331
skipping SAM header line:   @SQ SN:MWPT01000510.1   LN:1983864
skipping SAM header line:   @SQ SN:KV918371.1   LN:1956835
skipping SAM header line:   @SQ SN:KV918372.1   LN:3086374
skipping SAM header line:   @SQ SN:KV918373.1   LN:3420601
skipping SAM header line:   @SQ SN:KV918374.1   LN:1975111
skipping SAM header line:   @SQ SN:MWPT01000522.1   LN:1408919
skipping SAM header line:   @SQ SN:KV918375.1   LN:2529433
skipping SAM header line:   @SQ SN:KV918376.1   LN:1290748
skipping SAM header line:   @SQ SN:KV918377.1   LN:2437656
skipping SAM header line:   @SQ SN:MWPT01000531.1   LN:1154204
skipping SAM header line:   @SQ SN:KV918378.1   LN:1139503
skipping SAM header line:   @SQ SN:MWPT01000536.1   LN:868008
skipping SAM header line:   @SQ SN:MWPT01000537.1   LN:771245
skipping SAM header line:   @SQ SN:KV918379.1   LN:1322005
skipping SAM header line:   @SQ SN:KV918380.1   LN:1966111
skipping SAM header line:   @SQ SN:MWPT01000546.1   LN:662674
skipping SAM header line:   @SQ SN:KV918381.1   LN:1109647
skipping SAM header line:   @SQ SN:KV918382.1   LN:871299
skipping SAM header line:   @SQ SN:MWPT01000551.1   LN:451986
skipping SAM header line:   @SQ SN:MWPT01000552.1   LN:323820
skipping SAM header line:   @SQ SN:MWPT01000553.1   LN:248130
skipping SAM header line:   @SQ SN:MWPT01000240.1   LN:21598
skipping SAM header line:   @SQ SN:KV918383.1   LN:3521928
skipping SAM header line:   @SQ SN:KV918384.1   LN:978841
skipping SAM header line:   @SQ SN:KV918385.1   LN:9025367
skipping SAM header line:   @SQ SN:MWPT01000562.1   LN:6788731
skipping SAM header line:   @SQ SN:MWPT01000563.1   LN:4429963
skipping SAM header line:   @SQ SN:KV918386.1   LN:3718566
skipping SAM header line:   @SQ SN:MWPT01000566.1   LN:2001120
skipping SAM header line:   @SQ SN:MWPT01000567.1   LN:1613306
skipping SAM header line:   @SQ SN:MWPT01000568.1   LN:1271813
skipping SAM header line:   @SQ SN:MWPT01000569.1   LN:1139655
skipping SAM header line:   @SQ SN:KV918387.1   LN:1748706
skipping SAM header line:   @SQ SN:KV918388.1   LN:1215097
skipping SAM header line:   @SQ SN:KV918389.1   LN:1703051
skipping SAM header line:   @SQ SN:MWPT01000577.1   LN:293636
skipping SAM header line:   @SQ SN:MWPT01000578.1   LN:295967
skipping SAM header line:   @SQ SN:MWPT01000072.1   LN:5034843
skipping SAM header line:   @SQ SN:KV918390.1   LN:3800859
skipping SAM header line:   @SQ SN:KV918391.1   LN:6003931
skipping SAM header line:   @SQ SN:KV918392.1   LN:2421970
skipping SAM header line:   @SQ SN:KV918393.1   LN:3397556
skipping SAM header line:   @SQ SN:KV918394.1   LN:2301794
skipping SAM header line:   @SQ SN:MWPT01000091.1   LN:2010889
skipping SAM header line:   @SQ SN:MWPT01000092.1   LN:1561902
skipping SAM header line:   @SQ SN:KV918395.1   LN:3939623
skipping SAM header line:   @SQ SN:KV918396.1   LN:2232430
skipping SAM header line:   @SQ SN:MWPT01000100.1   LN:1208491
skipping SAM header line:   @SQ SN:KV918397.1   LN:1229882
skipping SAM header line:   @SQ SN:MWPT01000103.1   LN:1025708
skipping SAM header line:   @SQ SN:MWPT01000104.1   LN:844690
skipping SAM header line:   @SQ SN:MWPT01000105.1   LN:846079
skipping SAM header line:   @SQ SN:KV918398.1   LN:863292
skipping SAM header line:   @SQ SN:MWPT01000108.1   LN:789389
skipping SAM header line:   @SQ SN:KV918399.1   LN:1241954
skipping SAM header line:   @SQ SN:KV918400.1   LN:916510
skipping SAM header line:   @SQ SN:KV918401.1   LN:671914
skipping SAM header line:   @SQ SN:KV918402.1   LN:729568
skipping SAM header line:   @SQ SN:KV918403.1   LN:549473
skipping SAM header line:   @SQ SN:KV918404.1   LN:160532
skipping SAM header line:   @SQ SN:MWPT01000579.1   LN:2935297
skipping SAM header line:   @SQ SN:KV918405.1   LN:5824940
skipping SAM header line:   @SQ SN:KV918406.1   LN:2707926
skipping SAM header line:   @SQ SN:KV918407.1   LN:3442549
skipping SAM header line:   @SQ SN:MWPT01000590.1   LN:1838142
skipping SAM header line:   @SQ SN:MWPT01000591.1   LN:1545713
skipping SAM header line:   @SQ SN:MWPT01000592.1   LN:1371629
skipping SAM header line:   @SQ SN:KV918408.1   LN:1462725
skipping SAM header line:   @SQ SN:MWPT01000595.1   LN:1312981
skipping SAM header line:   @SQ SN:MWPT01000596.1   LN:1285219
skipping SAM header line:   @SQ SN:MWPT01000597.1   LN:1227422
skipping SAM header line:   @SQ SN:KV918409.1   LN:1203654
skipping SAM header line:   @SQ SN:MWPT01000600.1   LN:1196254
skipping SAM header line:   @SQ SN:MWPT01000601.1   LN:1154798
skipping SAM header line:   @SQ SN:KV918410.1   LN:1085728
skipping SAM header line:   @SQ SN:MWPT01000604.1   LN:1073738
skipping SAM header line:   @SQ SN:MWPT01000605.1   LN:899834
skipping SAM header line:   @SQ SN:MWPT01000606.1   LN:900897
skipping SAM header line:   @SQ SN:MWPT01000607.1   LN:849686
skipping SAM header line:   @SQ SN:KV918411.1   LN:1258750
skipping SAM header line:   @SQ SN:KV918412.1   LN:1120238
skipping SAM header line:   @SQ SN:MWPT01000613.1   LN:760141
skipping SAM header line:   @SQ SN:MWPT01000614.1   LN:778878
skipping SAM header line:   @SQ SN:KV918413.1   LN:1402054
skipping SAM header line:   @SQ SN:KV918414.1   LN:1077603
skipping SAM header line:   @SQ SN:KV918415.1   LN:749799
skipping SAM header line:   @SQ SN:MWPT01000625.1   LN:722770
skipping SAM header line:   @SQ SN:MWPT01000626.1   LN:678901
skipping SAM header line:   @SQ SN:MWPT01000627.1   LN:669847
skipping SAM header line:   @SQ SN:MWPT01000628.1   LN:667292
skipping SAM header line:   @SQ SN:MWPT01000629.1   LN:642728
skipping SAM header line:   @SQ SN:MWPT01000630.1   LN:633911
skipping SAM header line:   @SQ SN:MWPT01000631.1   LN:660918
skipping SAM header line:   @SQ SN:MWPT01000632.1   LN:580050
skipping SAM header line:   @SQ SN:MWPT01000633.1   LN:613152
skipping SAM header line:   @SQ SN:KV918416.1   LN:844482
skipping SAM header line:   @SQ SN:MWPT01000636.1   LN:568697
skipping SAM header line:   @SQ SN:MWPT01000637.1   LN:538392
skipping SAM header line:   @SQ SN:MWPT01000638.1   LN:547116
skipping SAM header line:   @SQ SN:MWPT01000639.1   LN:558824
skipping SAM header line:   @SQ SN:MWPT01000640.1   LN:520851
skipping SAM header line:   @SQ SN:MWPT01000641.1   LN:477734
skipping SAM header line:   @SQ SN:MWPT01000642.1   LN:459272
skipping SAM header line:   @SQ SN:MWPT01000643.1   LN:443597
skipping SAM header line:   @SQ SN:MWPT01000644.1   LN:419018
skipping SAM header line:   @SQ SN:MWPT01000645.1   LN:366979
skipping SAM header line:   @SQ SN:MWPT01000646.1   LN:347696
skipping SAM header line:   @SQ SN:KV918417.1   LN:563568
skipping SAM header line:   @SQ SN:MWPT01000649.1   LN:350730
skipping SAM header line:   @SQ SN:MWPT01000650.1   LN:326770
skipping SAM header line:   @SQ SN:MWPT01000651.1   LN:323883
skipping SAM header line:   @SQ SN:MWPT01000652.1   LN:306033
skipping SAM header line:   @SQ SN:MWPT01000653.1   LN:253517
skipping SAM header line:   @SQ SN:MWPT01000654.1   LN:211301
skipping SAM header line:   @SQ SN:KV918418.1   LN:476935
skipping SAM header line:   @SQ SN:KV918419.1   LN:259728
skipping SAM header line:   @SQ SN:MWPT01000660.1   LN:194985
skipping SAM header line:   @SQ SN:MWPT01000661.1   LN:172347
skipping SAM header line:   @SQ SN:MWPT01000662.1   LN:120632
skipping SAM header line:   @SQ SN:KV918420.1   LN:154501
skipping SAM header line:   @SQ SN:KV918421.1   LN:125890
skipping SAM header line:   @SQ SN:MWPT01000667.1   LN:73767
skipping SAM header line:   @SQ SN:KV918422.1   LN:125540
skipping SAM header line:   @SQ SN:MWPT01000670.1   LN:67795
skipping SAM header line:   @PG ID:Bismark  VN:v0.16.3  CL:"bismark --non_directional --multicore 9 -N 1 -q --genome /home/srlab/Documents/C-virginica-BSSeq/genome --se hard-trimmed-2112_lane1_TTAGGC_L001_R1.fastq -o /home/srlab/Documents/C-virginica-BSSeq/nd_hard-trimmed-2112_lane1_TTAGGC"
Processed lines: 500000
Processed lines: 1000000
Processed lines: 1500000
Processed lines: 2000000
Processed lines: 2500000
Processed lines: 3000000
Processed lines: 3500000
Processed lines: 4000000
Processed lines: 4500000
Processed lines: 5000000
Processed lines: 5500000
Processed lines: 6000000

Processed 6408819 lines in total
Total number of methylation call strings processed: 6408819

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   110732531

Total methylated C's in CpG context:    15974869
Total methylated C's in CHG context:    3940972
Total methylated C's in CHH context:    12123466

Total C to T conversions in CpG context:    6493550
Total C to T conversions in CHG context:    24822262
Total C to T conversions in CHH context:    47377412

C methylated in CpG context:    71.1%
C methylated in non-CpG context:    18.2%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 85

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: 85

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_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->  kept
CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->    kept
CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->  kept
Non_CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt contains data ->    kept
Non_CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bam.txt contains data ->  kept


Using these input files: CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt Non_CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt Non_CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt Non_CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt Non_CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bam.txt

Summary of parameters for bismark2bedGraph conversion:
======================================================
bedGraph output:        hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz
output directory:       ><
remove whitespaces:     no
CX context:         no (CpG context only, default)
No-header selected:     no
Sorting method:         Unix sort-based (smaller memory footprint, but slower)
Sort buffer size:       2G
Coverage threshold:     1
=============================================================================
Methylation information will now be written into a bedGraph and coverage file
=============================================================================

/home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt   /home/srlab/Documents/C-virginica-BSSeq/MethylationExtraction/CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt

Using the following files as Input:
Writing bedGraph to file: hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz
Also writing out a coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bismark.cov.gz
Also writing out a 0-based, half-open coverage file including counts methylated and unmethylated residues to file: hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz.bismark.zero.cov

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 hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished writing methylation calls from CpG_OT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOT_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_CTOB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt to merged temp file
Finished writing methylation calls from CpG_OB_hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.txt to merged temp file
Sorting input file hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged by positions (using -S of 2G)
Successfully deleted the temporary input file hard-trimmed-2112_lane1_TTAGGC_L001_R1_bismark_bt2.bedGraph.gz.methylation_calls.merged

Finished BedGraph conversion ...

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