Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/031920-trimtest-nod/tgd/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v01/<
CX context:					no (CpG context only, default)
Pooling CpG top/bottom strand evidence:		yes
Genome coordinates used:			0-based (user specified)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v01/

chr Scaffold_01 (89643857 bp)
chr Scaffold_02 (69596280 bp)
chr Scaffold_03 (57743597 bp)
chr Scaffold_04 (65288255 bp)
chr Scaffold_05 (67248332 bp)
chr Scaffold_06 (61759565 bp)
chr Scaffold_07 (43120122 bp)
chr Scaffold_08 (61151155 bp)
chr Scaffold_09 (38581958 bp)
chr Scaffold_10 (53961475 bp)
chr Scaffold_11 (51449921 bp)
chr Scaffold_12 (50438331 bp)
chr Scaffold_13 (44396874 bp)
chr Scaffold_14 (45393038 bp)
chr Scaffold_15 (47938513 bp)
chr Scaffold_16 (31980953 bp)
chr Scaffold_17 (34923512 bp)
chr Scaffold_18 (27737463 bp)

Stored sequence information of 18 chromosomes/scaffolds in total

==============================================================================
Methylation information will now be written into a genome-wide cytosine report
==============================================================================

>>> Writing genome-wide cytosine report to: EPI-167_S10_L002.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: Scaffold_01
Writing cytosine report for chromosome Scaffold_01 (stored 886466 different covered positions)
Writing cytosine report for chromosome Scaffold_02 (stored 685044 different covered positions)
Writing cytosine report for chromosome Scaffold_03 (stored 545794 different covered positions)
Writing cytosine report for chromosome Scaffold_04 (stored 620585 different covered positions)
Writing cytosine report for chromosome Scaffold_05 (stored 558238 different covered positions)
Writing cytosine report for chromosome Scaffold_06 (stored 546381 different covered positions)
Writing cytosine report for chromosome Scaffold_07 (stored 400888 different covered positions)
Writing cytosine report for chromosome Scaffold_08 (stored 559252 different covered positions)
Writing cytosine report for chromosome Scaffold_09 (stored 353227 different covered positions)
Writing cytosine report for chromosome Scaffold_10 (stored 474809 different covered positions)
Writing cytosine report for chromosome Scaffold_11 (stored 455613 different covered positions)
Writing cytosine report for chromosome Scaffold_12 (stored 495355 different covered positions)
Writing cytosine report for chromosome Scaffold_13 (stored 396884 different covered positions)
Writing cytosine report for chromosome Scaffold_14 (stored 505179 different covered positions)
Writing cytosine report for chromosome Scaffold_15 (stored 398495 different covered positions)
Writing cytosine report for chromosome Scaffold_16 (stored 319030 different covered positions)
Writing cytosine report for chromosome Scaffold_17 (stored 341268 different covered positions)
Writing cytosine report for last chromosome Scaffold_18 (stored 245950 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 18 chromosomes/scaffolds in total)

Now processing chromosomes that were not covered by any methylation calls in the coverage file...
All chromosomes in the genome were covered by at least some reads. coverage2cytosine processing complete.

Now merging top and bottom strand CpGs into a single CG dinucleotide entity (reading from file >>EPI-167_S10_L002.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to EPI-167_S10_L002.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!