Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 683967 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 526691 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 427770 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 487780 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 451611 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 429282 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 318097 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 442280 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 276863 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 374867 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 360907 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 381777 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 314657 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 400406 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 323605 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 246857 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 269611 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 201565 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 882980 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 680452 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 554186 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 624534 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 581425 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 553054 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 406547 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 570514 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 356464 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 486447 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 460873 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 496930 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 404555 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 516864 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 412731 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 316354 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 345191 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 257295 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 1124928 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 867426 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 703872 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 800887 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 742357 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 711341 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 519122 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 725094 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 452793 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 610034 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 596103 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 630685 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 513747 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 644318 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 530426 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 407889 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 439682 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 327872 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 853730 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 657358 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 535233 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 601305 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 556161 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 535847 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 398872 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 553684 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 346199 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 467113 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 449083 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 472259 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 391299 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 494841 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 404980 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 304541 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 333445 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 249244 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 713643 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 550665 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 448743 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 505660 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 464328 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 451698 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 331337 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 459691 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 290059 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 391606 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 376141 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 400268 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 327878 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 417298 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 334997 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 257323 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 280564 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 209497 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 752898 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 575740 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 469794 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 534612 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 491536 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 474023 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 349723 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 486052 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 302539 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 409478 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 397620 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 420462 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 344595 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 441298 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 355380 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 269859 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 295334 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 219684 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 616553 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 474657 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 386624 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 435241 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 401557 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 387385 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 286850 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 398321 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 250759 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 336251 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 325411 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 343950 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 284455 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 358942 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 287230 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 220482 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 244273 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 178642 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.

Summary of parameters for genome-wide cytosine report:
==============================================================================
Coverage infile:				/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz
Output directory:				><
Parent directory:				>/gscratch/scrubbed/strigg/analyses/20190806_v074/<
Genome directory:				>/gscratch/srlab/sr320/data/geoduck/v074/<
CX context:					no (CpG context only, default)
Genome coordinates used:			1-based (default)
GZIP compression:				yes
Split by chromosome:				no


Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/geoduck/v074/

chr PGA_scaffold1__77_contigs__length_89643857 (89643857 bp)
chr PGA_scaffold2__36_contigs__length_69596280 (69596280 bp)
chr PGA_scaffold3__111_contigs__length_57743597 (57743597 bp)
chr PGA_scaffold4__129_contigs__length_65288255 (65288255 bp)
chr PGA_scaffold5__109_contigs__length_67248332 (67248332 bp)
chr PGA_scaffold6__104_contigs__length_61759565 (61759565 bp)
chr PGA_scaffold7__69_contigs__length_43120122 (43120122 bp)
chr PGA_scaffold8__63_contigs__length_61151155 (61151155 bp)
chr PGA_scaffold9__45_contigs__length_38581958 (38581958 bp)
chr PGA_scaffold10__49_contigs__length_53961475 (53961475 bp)
chr PGA_scaffold11__79_contigs__length_51449921 (51449921 bp)
chr PGA_scaffold12__71_contigs__length_50438331 (50438331 bp)
chr PGA_scaffold13__52_contigs__length_44396874 (44396874 bp)
chr PGA_scaffold14__91_contigs__length_45393038 (45393038 bp)
chr PGA_scaffold15__101_contigs__length_47938513 (47938513 bp)
chr PGA_scaffold16__33_contigs__length_31980953 (31980953 bp)
chr PGA_scaffold17__51_contigs__length_34923512 (34923512 bp)
chr PGA_scaffold18__69_contigs__length_27737463 (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: /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_cytosine_CpG_cov_report.CpG_report.txt.gz <<<

Writing cytosine report for chromosome PGA_scaffold1__77_contigs__length_89643857 (stored 699756 different covered positions)
Writing cytosine report for chromosome PGA_scaffold2__36_contigs__length_69596280 (stored 540138 different covered positions)
Writing cytosine report for chromosome PGA_scaffold3__111_contigs__length_57743597 (stored 440496 different covered positions)
Writing cytosine report for chromosome PGA_scaffold4__129_contigs__length_65288255 (stored 498806 different covered positions)
Writing cytosine report for chromosome PGA_scaffold5__109_contigs__length_67248332 (stored 457650 different covered positions)
Writing cytosine report for chromosome PGA_scaffold6__104_contigs__length_61759565 (stored 446635 different covered positions)
Writing cytosine report for chromosome PGA_scaffold7__69_contigs__length_43120122 (stored 326734 different covered positions)
Writing cytosine report for chromosome PGA_scaffold8__63_contigs__length_61151155 (stored 454787 different covered positions)
Writing cytosine report for chromosome PGA_scaffold9__45_contigs__length_38581958 (stored 284659 different covered positions)
Writing cytosine report for chromosome PGA_scaffold10__49_contigs__length_53961475 (stored 382708 different covered positions)
Writing cytosine report for chromosome PGA_scaffold11__79_contigs__length_51449921 (stored 372893 different covered positions)
Writing cytosine report for chromosome PGA_scaffold12__71_contigs__length_50438331 (stored 391070 different covered positions)
Writing cytosine report for chromosome PGA_scaffold13__52_contigs__length_44396874 (stored 322699 different covered positions)
Writing cytosine report for chromosome PGA_scaffold14__91_contigs__length_45393038 (stored 413933 different covered positions)
Writing cytosine report for chromosome PGA_scaffold15__101_contigs__length_47938513 (stored 330185 different covered positions)
Writing cytosine report for chromosome PGA_scaffold16__33_contigs__length_31980953 (stored 252139 different covered positions)
Writing cytosine report for chromosome PGA_scaffold17__51_contigs__length_34923512 (stored 277692 different covered positions)
Writing cytosine report for last chromosome PGA_scaffold18__69_contigs__length_27737463 (stored 205805 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.