*** Bismark methylation extractor version v0.16.0 ***

Trying to determine the type of mapping from the SAM header line of file test_data_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
Output will be written to the current directory ('/spin1/users/user/bismark_test')

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_test_data_bismark_bt2.txt

Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_test_data_bismark_bt2.txt

Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_test_data_bismark_bt2.txt
Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_test_data_bismark_bt2.txt

Now reading in Bismark result file test_data_bismark_bt2.bam
skipping SAM header line:	@HD	VN:1.0	SO:unsorted
skipping SAM header line:	@SQ	SN:chrX	LN:155270560
skipping SAM header line:	@SQ	SN:chrY	LN:59373566
skipping SAM header line:	@PG	ID:Bismark	VN:v0.16.1	CL:"bismark XandY test_data.fastq"

Processed 378 lines in total
Total number of methylation call strings processed: 378

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	3258

Total methylated C's in CpG context:	88
Total methylated C's in CHG context:	4
Total methylated C's in CHH context:	13

Total C to T conversions in CpG context:	108
Total C to T conversions in CHG context:	777
Total C to T conversions in CHH context:	2268

C methylated in CpG context:	44.9%
C methylated in CHG context:	0.5%
C methylated in CHH context:	0.6%


Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 50

Determining maximum read length for M-Bias plot
Maximum read length of Read 1: 50

Deleting unused files ...

CpG_OT_test_data_bismark_bt2.txt contains data ->	kept
CpG_CTOT_test_data_bismark_bt2.txt was empty ->	deleted
CpG_CTOB_test_data_bismark_bt2.txt was empty ->	deleted
CpG_OB_test_data_bismark_bt2.txt contains data ->	kept
CHG_OT_test_data_bismark_bt2.txt contains data ->	kept
CHG_CTOT_test_data_bismark_bt2.txt was empty ->	deleted
CHG_CTOB_test_data_bismark_bt2.txt was empty ->	deleted
CHG_OB_test_data_bismark_bt2.txt contains data ->	kept
CHH_OT_test_data_bismark_bt2.txt contains data ->	kept
CHH_CTOT_test_data_bismark_bt2.txt was empty ->	deleted
CHH_CTOB_test_data_bismark_bt2.txt was empty ->	deleted
CHH_OB_test_data_bismark_bt2.txt contains data ->	kept