Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				Sealice_F1_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020320-cal/<
Genome directory:				>/gscratch/srlab/sr320/data/caligus/genome/<
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/caligus/genome/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 bp)

Stored sequence information of 21 chromosomes/scaffolds in total

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

>>> Writing genome-wide cytosine report to: Sealice_F1_S20_L001.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: Cr_scaffold0000001
Writing cytosine report for chromosome Cr_scaffold0000001 (stored 1152014 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000002 (stored 1072961 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000003 (stored 1024584 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000004 (stored 993465 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000005 (stored 930307 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000006 (stored 950022 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000007 (stored 924768 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000008 (stored 836658 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000009 (stored 761324 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000010 (stored 773537 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000011 (stored 1215621 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000012 (stored 698470 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000013 (stored 660817 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000014 (stored 695614 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000015 (stored 616875 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000016 (stored 577612 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000017 (stored 556771 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000018 (stored 444741 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000019 (stored 502996 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000020 (stored 265906 different covered positions)
Writing cytosine report for last chromosome Cr_scaffold0000021 (stored 267196 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 21 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 >>Sealice_F1_S20_L001.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Sealice_F1_S20_L001.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:				Sealice_F1_S20_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020320-cal/<
Genome directory:				>/gscratch/srlab/sr320/data/caligus/genome/<
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/caligus/genome/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 bp)

Stored sequence information of 21 chromosomes/scaffolds in total

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

>>> Writing genome-wide cytosine report to: Sealice_F1_S20_L002.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: Cr_scaffold0000001
Writing cytosine report for chromosome Cr_scaffold0000001 (stored 1147486 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000002 (stored 1067510 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000003 (stored 1019582 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000004 (stored 990582 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000005 (stored 926555 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000006 (stored 945263 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000007 (stored 922086 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000008 (stored 834091 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000009 (stored 757727 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000010 (stored 768986 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000011 (stored 1210060 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000012 (stored 694149 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000013 (stored 657521 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000014 (stored 691895 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000015 (stored 613768 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000016 (stored 574174 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000017 (stored 554589 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000018 (stored 442504 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000019 (stored 501235 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000020 (stored 264282 different covered positions)
Writing cytosine report for last chromosome Cr_scaffold0000021 (stored 266939 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 21 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 >>Sealice_F1_S20_L002.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Sealice_F1_S20_L002.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:				Sealice_F2_S22_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020320-cal/<
Genome directory:				>/gscratch/srlab/sr320/data/caligus/genome/<
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/caligus/genome/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 bp)

Stored sequence information of 21 chromosomes/scaffolds in total

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

>>> Writing genome-wide cytosine report to: Sealice_F2_S22_L001.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: Cr_scaffold0000001
Writing cytosine report for chromosome Cr_scaffold0000001 (stored 921363 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000002 (stored 850219 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000003 (stored 813573 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000004 (stored 797879 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000005 (stored 740405 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000006 (stored 762459 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000007 (stored 733584 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000008 (stored 662325 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000009 (stored 607300 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000010 (stored 619010 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000011 (stored 983586 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000012 (stored 555428 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000013 (stored 525266 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000014 (stored 548181 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000015 (stored 493908 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000016 (stored 461341 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000017 (stored 443492 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000018 (stored 353851 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000019 (stored 411183 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000020 (stored 214269 different covered positions)
Writing cytosine report for last chromosome Cr_scaffold0000021 (stored 218695 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 21 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 >>Sealice_F2_S22_L001.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Sealice_F2_S22_L001.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:				Sealice_F2_S22_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/sr320/020320-cal/<
Genome directory:				>/gscratch/srlab/sr320/data/caligus/genome/<
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/caligus/genome/

chr Cr_scaffold0000001 (36897007 bp)
chr Cr_scaffold0000002 (35124817 bp)
chr Cr_scaffold0000003 (33138466 bp)
chr Cr_scaffold0000004 (31456035 bp)
chr Cr_scaffold0000005 (30612693 bp)
chr Cr_scaffold0000006 (30259679 bp)
chr Cr_scaffold0000007 (29872177 bp)
chr Cr_scaffold0000008 (27803016 bp)
chr Cr_scaffold0000009 (25126635 bp)
chr Cr_scaffold0000010 (24815513 bp)
chr Cr_scaffold0000011 (35794548 bp)
chr Cr_scaffold0000012 (22957860 bp)
chr Cr_scaffold0000013 (21502856 bp)
chr Cr_scaffold0000014 (21148584 bp)
chr Cr_scaffold0000015 (19091682 bp)
chr Cr_scaffold0000016 (18525937 bp)
chr Cr_scaffold0000017 (17562062 bp)
chr Cr_scaffold0000018 (14680182 bp)
chr Cr_scaffold0000019 (14290452 bp)
chr Cr_scaffold0000020 (8286978 bp)
chr Cr_scaffold0000021 (8023048 bp)

Stored sequence information of 21 chromosomes/scaffolds in total

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

>>> Writing genome-wide cytosine report to: Sealice_F2_S22_L002.CpG_report.txt <<<

Storing all covered cytosine positions for chromosome: Cr_scaffold0000001
Writing cytosine report for chromosome Cr_scaffold0000001 (stored 917439 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000002 (stored 846941 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000003 (stored 809197 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000004 (stored 793721 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000005 (stored 737343 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000006 (stored 757037 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000007 (stored 729415 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000008 (stored 659209 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000009 (stored 603212 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000010 (stored 615160 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000011 (stored 979073 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000012 (stored 551259 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000013 (stored 521344 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000014 (stored 546013 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000015 (stored 490930 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000016 (stored 457177 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000017 (stored 440814 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000018 (stored 351457 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000019 (stored 408547 different covered positions)
Writing cytosine report for chromosome Cr_scaffold0000020 (stored 212318 different covered positions)
Writing cytosine report for last chromosome Cr_scaffold0000021 (stored 216908 different covered positions)
Finished writing out cytosine report for covered chromosomes (processed 21 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 >>Sealice_F2_S22_L002.CpG_report.txt<<, in output directory '')
>>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to Sealice_F2_S22_L002.CpG_report.merged_CpG_evidence.cov <<<

CpG merging complete. Good luck finding DMRs with bsseq!