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lcolladotor/fix-62551-out.txt

Created November 4, 2014 22:17
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fix-62551-out.txt
> library('derfinder')
>
> ## Set global species option
> options(species = 'canis_familiaris')
>
> ## Load data
> bam <- rep('10_130-chr11.bam', 6)
> names(bam) <- paste0('Sample', 1:6)
> fullCov <- fullCoverage(bam, chrs = c(1:38, 'X'))
2014-11-04 17:13:20 fullCoverage: processing chromosome 1
2014-11-04 17:13:20 loadCoverage: finding chromosome lengths
2014-11-04 17:13:20 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:20 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:20 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:21 filterData: originally there were 122678785 rows, now there are 122678785 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:21 fullCoverage: processing chromosome 2
2014-11-04 17:13:21 loadCoverage: finding chromosome lengths
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:21 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:21 filterData: originally there were 85426708 rows, now there are 85426708 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:21 fullCoverage: processing chromosome 3
2014-11-04 17:13:22 loadCoverage: finding chromosome lengths
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:22 filterData: originally there were 91889043 rows, now there are 91889043 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:22 fullCoverage: processing chromosome 4
2014-11-04 17:13:22 loadCoverage: finding chromosome lengths
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:22 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:22 filterData: originally there were 88276631 rows, now there are 88276631 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:22 fullCoverage: processing chromosome 5
2014-11-04 17:13:22 loadCoverage: finding chromosome lengths
2014-11-04 17:13:22 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:23 filterData: originally there were 88915250 rows, now there are 88915250 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:23 fullCoverage: processing chromosome 6
2014-11-04 17:13:23 loadCoverage: finding chromosome lengths
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:23 filterData: originally there were 77573801 rows, now there are 77573801 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:23 fullCoverage: processing chromosome 7
2014-11-04 17:13:23 loadCoverage: finding chromosome lengths
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:23 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:24 filterData: originally there were 80974532 rows, now there are 80974532 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:24 fullCoverage: processing chromosome 8
2014-11-04 17:13:24 loadCoverage: finding chromosome lengths
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:24 filterData: originally there were 74330416 rows, now there are 74330416 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:24 fullCoverage: processing chromosome 9
2014-11-04 17:13:24 loadCoverage: finding chromosome lengths
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:24 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:25 filterData: originally there were 61074082 rows, now there are 61074082 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:25 fullCoverage: processing chromosome 10
2014-11-04 17:13:25 loadCoverage: finding chromosome lengths
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:25 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:25 filterData: originally there were 69331447 rows, now there are 69331447 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:25 fullCoverage: processing chromosome 11
2014-11-04 17:13:25 loadCoverage: finding chromosome lengths
2014-11-04 17:13:25 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:29 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:31 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:33 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:34 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:36 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:37 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:38 filterData: originally there were 74389097 rows, now there are 74389097 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:38 fullCoverage: processing chromosome 12
2014-11-04 17:13:38 loadCoverage: finding chromosome lengths
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:38 filterData: originally there were 72498081 rows, now there are 72498081 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:38 fullCoverage: processing chromosome 13
2014-11-04 17:13:38 loadCoverage: finding chromosome lengths
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:38 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:39 filterData: originally there were 63241923 rows, now there are 63241923 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:39 fullCoverage: processing chromosome 14
2014-11-04 17:13:39 loadCoverage: finding chromosome lengths
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:39 filterData: originally there were 60966679 rows, now there are 60966679 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:39 fullCoverage: processing chromosome 15
2014-11-04 17:13:39 loadCoverage: finding chromosome lengths
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:39 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:40 filterData: originally there were 64190966 rows, now there are 64190966 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:40 fullCoverage: processing chromosome 16
2014-11-04 17:13:40 loadCoverage: finding chromosome lengths
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:40 filterData: originally there were 59632846 rows, now there are 59632846 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:40 fullCoverage: processing chromosome 17
2014-11-04 17:13:40 loadCoverage: finding chromosome lengths
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:40 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:41 filterData: originally there were 64289059 rows, now there are 64289059 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:41 fullCoverage: processing chromosome 18
2014-11-04 17:13:41 loadCoverage: finding chromosome lengths
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:41 filterData: originally there were 55844845 rows, now there are 55844845 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:41 fullCoverage: processing chromosome 19
2014-11-04 17:13:41 loadCoverage: finding chromosome lengths
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:41 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:41 filterData: originally there were 53741614 rows, now there are 53741614 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:41 fullCoverage: processing chromosome 20
2014-11-04 17:13:41 loadCoverage: finding chromosome lengths
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:42 filterData: originally there were 58134056 rows, now there are 58134056 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:42 fullCoverage: processing chromosome 21
2014-11-04 17:13:42 loadCoverage: finding chromosome lengths
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:42 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:42 filterData: originally there were 50858623 rows, now there are 50858623 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:42 fullCoverage: processing chromosome 22
2014-11-04 17:13:42 loadCoverage: finding chromosome lengths
2014-11-04 17:13:42 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:43 filterData: originally there were 61439934 rows, now there are 61439934 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:43 fullCoverage: processing chromosome 23
2014-11-04 17:13:43 loadCoverage: finding chromosome lengths
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:43 filterData: originally there were 52294480 rows, now there are 52294480 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:43 fullCoverage: processing chromosome 24
2014-11-04 17:13:43 loadCoverage: finding chromosome lengths
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:43 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:44 filterData: originally there were 47698779 rows, now there are 47698779 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:44 fullCoverage: processing chromosome 25
2014-11-04 17:13:44 loadCoverage: finding chromosome lengths
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:44 filterData: originally there were 51628933 rows, now there are 51628933 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:44 fullCoverage: processing chromosome 26
2014-11-04 17:13:44 loadCoverage: finding chromosome lengths
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:44 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:45 filterData: originally there were 38964690 rows, now there are 38964690 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:45 fullCoverage: processing chromosome 27
2014-11-04 17:13:45 loadCoverage: finding chromosome lengths
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:45 filterData: originally there were 45876710 rows, now there are 45876710 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:45 fullCoverage: processing chromosome 28
2014-11-04 17:13:45 loadCoverage: finding chromosome lengths
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:45 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:46 filterData: originally there were 41182112 rows, now there are 41182112 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:46 fullCoverage: processing chromosome 29
2014-11-04 17:13:46 loadCoverage: finding chromosome lengths
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:46 filterData: originally there were 41845238 rows, now there are 41845238 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:46 fullCoverage: processing chromosome 30
2014-11-04 17:13:46 loadCoverage: finding chromosome lengths
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:46 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:47 filterData: originally there were 40214260 rows, now there are 40214260 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:47 fullCoverage: processing chromosome 31
2014-11-04 17:13:47 loadCoverage: finding chromosome lengths
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:47 filterData: originally there were 39895921 rows, now there are 39895921 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:47 fullCoverage: processing chromosome 32
2014-11-04 17:13:47 loadCoverage: finding chromosome lengths
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:47 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:48 filterData: originally there were 38810281 rows, now there are 38810281 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:48 fullCoverage: processing chromosome 33
2014-11-04 17:13:48 loadCoverage: finding chromosome lengths
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:48 filterData: originally there were 31377067 rows, now there are 31377067 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:48 fullCoverage: processing chromosome 34
2014-11-04 17:13:48 loadCoverage: finding chromosome lengths
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:48 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:49 filterData: originally there were 42124431 rows, now there are 42124431 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:49 fullCoverage: processing chromosome 35
2014-11-04 17:13:49 loadCoverage: finding chromosome lengths
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:49 filterData: originally there were 26524999 rows, now there are 26524999 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:49 fullCoverage: processing chromosome 36
2014-11-04 17:13:49 loadCoverage: finding chromosome lengths
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:49 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:49 filterData: originally there were 30810995 rows, now there are 30810995 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:49 fullCoverage: processing chromosome 37
2014-11-04 17:13:49 loadCoverage: finding chromosome lengths
2014-11-04 17:13:49 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:50 filterData: originally there were 30902991 rows, now there are 30902991 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:50 fullCoverage: processing chromosome 38
2014-11-04 17:13:50 loadCoverage: finding chromosome lengths
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:50 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:51 filterData: originally there were 23914537 rows, now there are 23914537 rows. Meaning that 0 percent was filtered.
2014-11-04 17:13:51 fullCoverage: processing chromosome X
2014-11-04 17:13:51 loadCoverage: finding chromosome lengths
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: loading BAM file 10_130-chr11.bam
2014-11-04 17:13:51 loadCoverage: applying the cutoff to the merged data
2014-11-04 17:13:51 filterData: originally there were 123869142 rows, now there are 123869142 rows. Meaning that 0 percent was filtered.
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species canis_familiaris
>
>
> ## Inspect chr names
> names(fullCov)
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9"
[10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18"
[19] "chr19" "chr20" "chr21" "chr22" "chr23" "chr24" "chr25" "chr26" "chr27"
[28] "chr28" "chr29" "chr30" "chr31" "chr32" "chr33" "chr34" "chr35" "chr36"
[37] "chr37" "chr38" "chrX"
>
> ## Filter
> filteredCov <- lapply(fullCov, filterData, cutoff = 2)
2014-11-04 17:14:12 filterData: originally there were 122678785 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 85426708 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 91889043 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 88276631 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 88915250 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 77573801 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:12 filterData: originally there were 80974532 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 74330416 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 61074082 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 69331447 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 74389097 rows, now there are 1444850 rows. Meaning that 98.06 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 72498081 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 63241923 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 60966679 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 64190966 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 59632846 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 64289059 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 55844845 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 53741614 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 58134056 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 50858623 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 61439934 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 52294480 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 47698779 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 51628933 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:13 filterData: originally there were 38964690 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 45876710 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 41182112 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 41845238 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 40214260 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 39895921 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 38810281 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 31377067 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 42124431 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 26524999 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 30810995 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 30902991 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 23914537 rows, now there are 0 rows. Meaning that 100 percent was filtered.
2014-11-04 17:14:14 filterData: originally there were 123869142 rows, now there are 0 rows. Meaning that 100 percent was filtered.
>
> ## Artificially copy data from chr11 to chr30
> filteredCov$chr30 <- filteredCov$chr11
>
> ## Change some values because we only have one sample
> for(sample in 2:6) {
+ set.seed(sample)
+ filteredCov$chr30$coverage[[sample]] <- filteredCov$chr30$coverage[[sample]] + round(runif(1, 0, 10))
+ }
>
>
> ## Setup
> perms <- 2
> currentChrom <- 'chr30'
> groups <- factor(rep(letters[1:3], each = 2))
> models <- list(
+ mod = model.matrix( ~ groups ),
+ mod0 = model.matrix( ~0 + rep(1L, 6))
+ )
>
> ## Get results
> results <- analyzeChr(chr = currentChrom, filteredCov[[currentChrom]], models,
+ mc.cores=1, groupInfo = groups, writeOutput = TRUE, cutoffFstat = 0.5,
+ cutoffType = 'empirical', nPermute = perms,
+ seeds = 19731107 + seq_len(perms), lowMemDir = file.path(tempdir(), currentChrom),
+ returnOutput = TRUE, verbose = TRUE, runAnnotation = FALSE)
2014-11-04 17:14:26 analyzeChr: Pre-processing the coverage data
2014-11-04 17:14:27 preprocessCoverage: splitting the data
2014-11-04 17:14:42 analyzeChr: Calculating statistics
2014-11-04 17:14:42 calculateStats: calculating the F-statistics
2014-11-04 17:14:44 analyzeChr: Calculating pvalues
2014-11-04 17:14:44 analyzeChr: Using the following empirical cutoff for the F-statistics 1.03175496095696
2014-11-04 17:14:44 calculatePvalues: identifying data segments
2014-11-04 17:14:44 findRegions: segmenting F-stats information
2014-11-04 17:14:44 .getSegmentsRle: segmenting with cutoff(s) 1.03175496095696
2014-11-04 17:14:44 findRegions: identifying candidate DERs
2014-11-04 17:14:44 findRegions: identifying DER clusters
2014-11-04 17:15:08 calculatePvalues: calculating F-statistics for permutation 1 and seed 19731108
2014-11-04 17:15:09 findRegions: segmenting F-stats information
2014-11-04 17:15:09 .getSegmentsRle: segmenting with cutoff(s) 1.03175496095696
2014-11-04 17:15:09 findRegions: found no segments to work with!!
2014-11-04 17:15:09 calculatePvalues: calculating F-statistics for permutation 2 and seed 19731109
2014-11-04 17:15:10 findRegions: segmenting F-stats information
2014-11-04 17:15:10 .getSegmentsRle: segmenting with cutoff(s) 1.03175496095696
2014-11-04 17:15:10 findRegions: identifying candidate DERs
2014-11-04 17:15:11 calculatePvalues: calculating the p-values
2014-11-04 17:15:34 analyzeChr: Annotating regions
>
> ## Session information
> options(width = 90)
> devtools::session_info()
Session info-----------------------------------------------------------------------------
setting value
version R version 3.1.2 Patched (2014-11-01 r66923)
system x86_64, darwin10.8.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/New_York
Packages---------------------------------------------------------------------------------
package * version date source
acepack 1.3.3.3 2013-05-03 CRAN (R 3.1.0)
AnnotationDbi 1.28.1 2014-10-28 Bioconductor
base64enc 0.1.2 2014-06-26 CRAN (R 3.1.0)
BatchJobs 1.5 2014-10-30 CRAN (R 3.1.2)
BBmisc 1.8 2014-10-30 CRAN (R 3.1.2)
Biobase 2.26.0 2014-10-14 Bioconductor
BiocGenerics 0.12.0 2014-10-14 Bioconductor
BiocParallel 1.0.0 2014-10-15 Bioconductor
biomaRt 2.22.0 2014-10-14 Bioconductor
Biostrings 2.34.0 2014-10-14 Bioconductor
bitops 1.0.6 2013-08-17 CRAN (R 3.1.0)
brew 1.0.6 2011-04-13 CRAN (R 3.1.0)
bumphunter 1.6.0 2014-10-14 Bioconductor
checkmate 1.5.0 2014-10-19 CRAN (R 3.1.1)
cluster 1.15.3 2014-09-04 CRAN (R 3.1.2)
codetools 0.2.9 2014-08-21 CRAN (R 3.1.2)
colorout * 1.0.2 2014-11-03 local
DBI 0.3.1 2014-09-24 CRAN (R 3.1.1)
derfinder * 1.0.6 2014-11-04 Github (lcolladotor/derfinder@d316ee7)
derfinderHelper 1.0.3 2014-11-04 Github (lcolladotor/derfinderHelper@6f7ac88)
devtools 1.6.1 2014-10-07 CRAN (R 3.1.1)
digest 0.6.4 2013-12-03 CRAN (R 3.1.0)
doRNG 1.6 2014-03-07 CRAN (R 3.1.1)
fail 1.2 2013-09-19 CRAN (R 3.1.0)
foreach 1.4.2 2014-04-11 CRAN (R 3.1.0)
foreign 0.8.61 2014-03-28 CRAN (R 3.1.2)
Formula 1.1.2 2014-07-13 CRAN (R 3.1.1)
GenomeInfoDb 1.2.2 2014-10-26 Bioconductor
GenomicAlignments 1.2.0 2014-10-14 Bioconductor
GenomicFeatures 1.18.2 2014-10-28 Bioconductor
GenomicFiles 1.2.0 2014-10-14 Bioconductor
GenomicRanges 1.18.1 2014-10-16 Bioconductor
Hmisc 3.14.5 2014-09-12 CRAN (R 3.1.1)
IRanges 2.0.0 2014-10-14 Bioconductor
iterators 1.0.7 2014-04-11 CRAN (R 3.1.0)
lattice 0.20.29 2014-04-04 CRAN (R 3.1.2)
latticeExtra 0.6.26 2013-08-15 CRAN (R 3.1.0)
locfit 1.5.9.1 2013-04-20 CRAN (R 3.1.0)
Matrix 1.1.4 2014-06-15 CRAN (R 3.1.2)
matrixStats 0.10.3 2014-10-15 CRAN (R 3.1.1)
nnet 7.3.8 2014-03-28 CRAN (R 3.1.2)
pkgmaker 0.22 2014-05-14 CRAN (R 3.1.0)
qvalue 1.40.0 2014-10-14 Bioconductor
R.methodsS3 1.6.1 2014-01-05 CRAN (R 3.1.0)
RColorBrewer 1.0.5 2011-06-17 CRAN (R 3.1.0)
RCurl 1.95.4.3 2014-07-29 CRAN (R 3.1.1)
registry 0.2 2012-01-24 CRAN (R 3.1.0)
rngtools 1.2.4 2014-03-06 CRAN (R 3.1.0)
rpart 4.1.8 2014-03-28 CRAN (R 3.1.2)
Rsamtools 1.18.1 2014-10-24 Bioconductor
RSQLite 1.0.0 2014-10-25 CRAN (R 3.1.2)
rstudioapi 0.1 2014-03-27 CRAN (R 3.1.0)
rtracklayer 1.26.1 2014-10-18 Bioconductor
S4Vectors 0.4.0 2014-10-14 Bioconductor
sendmailR 1.2.1 2014-09-21 CRAN (R 3.1.1)
stringr 0.6.2 2012-12-06 CRAN (R 3.1.0)
survival 2.37.7 2014-01-22 CRAN (R 3.1.2)
XML 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
xtable 1.7.4 2014-09-12 CRAN (R 3.1.1)
XVector 0.6.0 2014-10-14 Bioconductor
zlibbioc 1.12.0 2014-10-14 Bioconductor
>
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