Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				../output/02.20-bismark-methylation-extraction/EF03-EM03-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/home/shared/8TB_HDD_03/sr320/github/ceasmallr/code/<
Genome directory:				>/home/shared/8TB_HDD_03/sr320/github/ceasmallr/data/genome/<
Coverage threshold				0 (all positions will be reported, default)
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: /home/shared/8TB_HDD_03/sr320/github/ceasmallr/data/genome/

chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Stored sequence information of 11 chromosomes/scaffolds in total

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

Adding context-specific methylation summaries

>>> Writing genome-wide cytosine report to: ../output/03-methylation/EF03-EM03-Zygote.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: ../output/03-methylation/EF03-EM03-Zygote.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 1251 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 1099963 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 1006954 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 1191623 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 998820 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1744080 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 656974 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 769649 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 1022777 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 1364652 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 427387 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 11 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 >>../output/03-methylation/EF03-EM03-Zygote.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to ../output/03-methylation/EF03-EM03-Zygote.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!