[bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 140 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 140 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 56 files and 28 in-memory blocks... [bam_sort_core] merging from 196 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 112 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... [bam_sort_core] merging from 84 files and 28 in-memory blocks... Summary of parameters for genome-wide cytosine report: ============================================================================== Coverage infile: 12M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 12M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035787.1 Writing cytosine report for chromosome NC_035787.1 (stored 2283366 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2250237 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2021624 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1009987 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3347376 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3096730 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2459811 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2017251 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1716154 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1478817 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 947 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 >>12M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 12M_R1_val_1.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: 13M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 13M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035780.1 Writing cytosine report for chromosome NC_035780.1 (stored 2267880 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2465296 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1582559 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3345680 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3062465 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2011533 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2016963 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1402020 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1024434 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2312370 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 957 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 >>13M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 13M_R1_val_1.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: 16F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 16F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035787.1 Writing cytosine report for chromosome NC_035787.1 (stored 2320628 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3111818 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2464396 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2269966 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2018030 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3337005 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1486010 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1000933 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1731853 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2007606 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1342 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 >>16F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 16F_R1_val_1.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: 19F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 19F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035784.1 Writing cytosine report for chromosome NC_035784.1 (stored 3358514 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2022168 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3086512 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2463550 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2295853 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2019939 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1011381 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1757 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1451946 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2264695 different covered positions) Writing cytosine report for last chromosome NC_035786.1 (stored 1693138 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 >>19F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 19F_R1_val_1.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: 22F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 22F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035786.1 Writing cytosine report for chromosome NC_035786.1 (stored 1654942 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2221195 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3270542 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2418823 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 968796 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2930692 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1982334 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1404609 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1621 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1958446 different covered positions) Writing cytosine report for last chromosome NC_035780.1 (stored 2211220 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 >>22F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 22F_R1_val_1.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: 23M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 23M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035780.1 Writing cytosine report for chromosome NC_035780.1 (stored 2262295 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3068137 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1712136 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2018067 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3382945 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2034276 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2301547 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2470140 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1482397 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1041473 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 936 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 >>23M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 23M_R1_val_1.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: 29F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 29F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035784.1 Writing cytosine report for chromosome NC_035784.1 (stored 3318709 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2239860 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3045922 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2281221 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1443303 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2420314 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1990432 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1990712 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1382 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1674522 different covered positions) Writing cytosine report for last chromosome NC_035789.1 (stored 1006870 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 >>29F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 29F_R1_val_1.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: 31M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 31M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035786.1 Writing cytosine report for chromosome NC_035786.1 (stored 1591087 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2332886 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2903195 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1972932 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3471369 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1936779 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2260712 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1392899 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 938085 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2129790 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 903 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 >>31M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 31M_R1_val_1.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: 35F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 35F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035785.1 Writing cytosine report for chromosome NC_035785.1 (stored 1426437 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1700145 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2446349 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3340828 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2256165 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3028099 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1007731 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2281384 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2016474 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1996555 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1757 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 >>35F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 35F_R1_val_1.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: 36F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 36F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035780.1 Writing cytosine report for chromosome NC_035780.1 (stored 2231041 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1709564 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2006036 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2002621 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3056174 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1446714 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2438237 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3313601 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2268610 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1681 different covered positions) Writing cytosine report for last chromosome NC_035789.1 (stored 1028710 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 >>36F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 36F_R1_val_1.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: 39F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 39F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035786.1 Writing cytosine report for chromosome NC_035786.1 (stored 1665743 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1972719 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2223253 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1006277 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2996548 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3331499 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2231429 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2421543 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1983347 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1431789 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1784 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 >>39F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 39F_R1_val_1.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: 3F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 3F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035787.1 Writing cytosine report for chromosome NC_035787.1 (stored 2266858 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2398132 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1987641 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1996021 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3365847 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1529082 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2218530 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1690836 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3096603 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1096579 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1630 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 >>3F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 3F_R1_val_1.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: 41F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 41F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035783.1 Writing cytosine report for chromosome NC_035783.1 (stored 1922861 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2154454 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1372409 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2133796 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1543872 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3228312 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1940753 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2893078 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2320502 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1390 different covered positions) Writing cytosine report for last chromosome NC_035789.1 (stored 936838 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 >>41F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 41F_R1_val_1.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: 44F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 44F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035784.1 Writing cytosine report for chromosome NC_035784.1 (stored 3521014 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2600554 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1105692 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3295447 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1838961 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2389880 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2132145 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2454438 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1554433 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2117041 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1565 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 >>44F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 44F_R1_val_1.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: 48M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 48M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035782.1 Writing cytosine report for chromosome NC_035782.1 (stored 2409593 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2987846 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2207955 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1663658 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1970760 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2213204 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1976220 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3271605 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 977735 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1424019 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 996 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 >>48M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 48M_R1_val_1.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: 50F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 50F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035784.1 Writing cytosine report for chromosome NC_035784.1 (stored 3319024 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2445190 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1028655 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2299695 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2001538 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1724895 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3079333 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1459903 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2248325 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2012085 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1593 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 >>50F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 50F_R1_val_1.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: 52F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 52F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035782.1 Writing cytosine report for chromosome NC_035782.1 (stored 2465745 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2326505 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2025700 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3375100 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3111708 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2022914 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1024020 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1714239 different covered positions) Writing cytosine report for chromosome NC_007175.2 (stored 1396 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2283206 different covered positions) Writing cytosine report for last chromosome NC_035785.1 (stored 1482645 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 >>52F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 52F_R1_val_1.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: 53F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 53F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035785.1 Writing cytosine report for chromosome NC_035785.1 (stored 1469356 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1697374 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2286229 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3357023 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2266137 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2023298 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2468371 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3087402 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2020729 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1020920 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1668 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 >>53F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 53F_R1_val_1.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: 54F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 54F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035782.1 Writing cytosine report for chromosome NC_035782.1 (stored 2476787 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3381733 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 2024609 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2263925 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 2023430 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2317586 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1700093 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1476619 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3047017 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1026291 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1501 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 >>54F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 54F_R1_val_1.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: 59M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 59M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035785.1 Writing cytosine report for chromosome NC_035785.1 (stored 1342825 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2146461 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1913600 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1901658 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3141612 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2834162 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2142337 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2306070 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 910124 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1538012 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 905 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 >>59M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 59M_R1_val_1.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: 64M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 64M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035782.1 Writing cytosine report for chromosome NC_035782.1 (stored 2408459 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2211476 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1984778 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2224056 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3298882 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1987920 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1005421 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1424250 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2975513 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1677372 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 955 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 >>64M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 64M_R1_val_1.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: 6M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 6M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035788.1 Writing cytosine report for chromosome NC_035788.1 (stored 2948362 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1938101 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2340704 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2169462 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1930489 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2179033 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3248885 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1380706 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 967419 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1646998 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 990 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 >>6M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 6M_R1_val_1.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: 76F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 76F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035789.1 Writing cytosine report for chromosome NC_035789.1 (stored 960357 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1988111 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2252044 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2158309 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1978663 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2428062 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3307622 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1675532 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 3003556 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1409504 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1581 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 >>76F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 76F_R1_val_1.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: 77F_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 77F_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035787.1 Writing cytosine report for chromosome NC_035787.1 (stored 2261644 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1997367 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 1011331 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2226752 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1986246 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1435977 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3287286 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2995144 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2417161 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1690288 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 1495 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 >>77F_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 77F_R1_val_1.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: 7M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 7M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035782.1 Writing cytosine report for chromosome NC_035782.1 (stored 2415057 different covered positions) Writing cytosine report for chromosome NC_035785.1 (stored 1421164 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1990315 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3332211 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2950399 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2250806 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 995649 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2221867 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1994301 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1650744 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 980 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 >>7M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 7M_R1_val_1.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: 9M_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz Output directory: >< Parent directory: >/gscratch/scrubbed/sr320/120321-cvBS/< 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 ============================================================================== >>> Writing genome-wide cytosine report to: 9M_R1_val_1.CpG_report.txt <<< Storing all covered cytosine positions for chromosome: NC_035785.1 Writing cytosine report for chromosome NC_035785.1 (stored 1376004 different covered positions) Writing cytosine report for chromosome NC_035788.1 (stored 2934386 different covered positions) Writing cytosine report for chromosome NC_035784.1 (stored 3323539 different covered positions) Writing cytosine report for chromosome NC_035780.1 (stored 2169193 different covered positions) Writing cytosine report for chromosome NC_035781.1 (stored 1966949 different covered positions) Writing cytosine report for chromosome NC_035782.1 (stored 2404901 different covered positions) Writing cytosine report for chromosome NC_035786.1 (stored 1664000 different covered positions) Writing cytosine report for chromosome NC_035787.1 (stored 2212185 different covered positions) Writing cytosine report for chromosome NC_035783.1 (stored 1963993 different covered positions) Writing cytosine report for chromosome NC_035789.1 (stored 877903 different covered positions) Writing cytosine report for last chromosome NC_007175.2 (stored 908 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 >>9M_R1_val_1.CpG_report.txt<<, in output directory '') >>> Writing a new coverage file with top and bottom strand CpG methylation evidence merged to 9M_R1_val_1.CpG_report.merged_CpG_evidence.cov <<< CpG merging complete. Good luck finding DMRs with bsseq!