Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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:			1-based (default)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-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: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 777 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 602195 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 557460 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 650735 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 548723 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 969891 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 331270 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 366722 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 539351 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 673842 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 212679 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 >>20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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:			1-based (default)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-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: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 850 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 862989 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 804105 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 943945 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 800183 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1399751 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 494750 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 537258 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 771746 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 991274 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 302399 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 >>20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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:			1-based (default)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-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: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 858 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 802237 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 734863 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 864032 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 725019 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1287432 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 451786 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 504002 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 723146 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 924031 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 286111 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 >>20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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:			1-based (default)
GZIP compression:				no
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cvirg-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: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 865 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 726170 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 667980 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 770348 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 655813 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1161172 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 403367 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 447389 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 641736 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 831002 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 245539 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 >>20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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: /gscratch/srlab/sr320/data/Cvirg-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: zb_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: zb_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 777 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 602195 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 557460 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 650735 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 548723 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 969891 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 331270 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 366722 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 539351 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 673842 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 212679 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 >>zb_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zb_20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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: /gscratch/srlab/sr320/data/Cvirg-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: zb_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: zb_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 850 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 862989 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 804105 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 943945 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 800183 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1399751 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 494750 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 537258 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 771746 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 991274 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 302399 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 >>zb_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zb_20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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: /gscratch/srlab/sr320/data/Cvirg-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: zb_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: zb_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 858 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 802237 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 734863 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 864032 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 725019 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1287432 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 451786 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 504002 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 723146 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 924031 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 286111 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 >>zb_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zb_20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020122-CMoil/<
Genome directory:				>/gscratch/srlab/sr320/data/Cvirg-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: /gscratch/srlab/sr320/data/Cvirg-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: zb_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.txt <<<

>>> Writing all cytosine context summary file to: zb_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.cytosine_context_summary.txt <<<

Storing all covered cytosine positions for chromosome: NC_007175.2
Writing cytosine report for chromosome NC_007175.2 (stored 865 different covered positions)
Writing cytosine report for chromosome NC_035780.1 (stored 726170 different covered positions)
Writing cytosine report for chromosome NC_035781.1 (stored 667980 different covered positions)
Writing cytosine report for chromosome NC_035782.1 (stored 770348 different covered positions)
Writing cytosine report for chromosome NC_035783.1 (stored 655813 different covered positions)
Writing cytosine report for chromosome NC_035784.1 (stored 1161172 different covered positions)
Writing cytosine report for chromosome NC_035785.1 (stored 403367 different covered positions)
Writing cytosine report for chromosome NC_035786.1 (stored 447389 different covered positions)
Writing cytosine report for chromosome NC_035787.1 (stored 641736 different covered positions)
Writing cytosine report for chromosome NC_035788.1 (stored 831002 different covered positions)
Writing cytosine report for last chromosome NC_035789.1 (stored 245539 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 >>zb_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to zb_20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!