*** Bismark methylation extractor version v0.25.0 ***

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 ('/data/$USER/bismark_test')

Checking file >>test_data_bismark_bt2.bam<< for signs of file truncation...

Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_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:v0.25.0      CL:"bismark XandY test_data.fastq"
skipping SAM header line:       @PG     ID:samtools     PN:samtools     PP:Bismark      VN:1.21 CL:/usr/local/apps/samtools/1.21/bin/samtools view -bSh -
skipping SAM header line:       @PG     ID:samtools.1   PN:samtools     PP:samtools     VN:1.21 CL:/usr/local/apps/samtools/1.21/bin/samtools view -h test_data_bismark_bt2.bam

Processed 355 lines in total
Total number of methylation call strings processed: 355

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   3032

Total methylated C's in CpG context:    79
Total methylated C's in CHG context:    4
Total methylated C's in CHH context:    10

Total C to T conversions in CpG context:        101
Total C to T conversions in CHG context:        709
Total C to T conversions in CHH context:        2129

C methylated in CpG context:    43.9%
C methylated in CHG context:    0.6%
C methylated in CHH context:    0.5%


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