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evaluated code record of regionMatrix issue, plus traceback and session info
Raw
regionmatrix_issue.txt
> ## Load libraries
> library('derfinder')
> library('GenomicRanges')
> file_designations <- c("WT1","WT2","WT3", "MT1", "MT2", "MT3")
> chrs_all = c('I', 'II','III','IV', 'IX', 'V', 'VI', 'VII', 'VIII', 'X', 'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI')
> ## Load the data from disk
> files <- file.path("/data/alignments", file_designations , paste0(file_designations,"Aligned.sorted.bam"))
> system.time(fullCov <- fullCoverage(files = files, chrs = chrs_all,
+ totalMapped = sapply(files,getTotalMapped, chrs = chrs_all), targetSize = 8e+07, species = "ReallySaccharomyces_cerevisiaeBUTiWANTtoSEEifCANgetREGIONMATRIXtoWORK")) # see http://www.astrostatistics.psu.edu/su07/R/html/base/html/sapply.html
2017-05-03 17:15:47 fullCoverage: processing chromosome I
2017-05-03 17:15:47 loadCoverage: finding chromosome lengths
2017-05-03 17:15:47 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:15:48 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:15:48 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:15:49 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:15:50 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:15:51 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:15:52 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:15:52 filterData: normalizing coverage
2017-05-03 17:15:52 filterData: done normalizing coverage
2017-05-03 17:15:52 filterData: originally there were 230218 rows, now there are 230218 rows. Meaning that 0 percent was filtered.
2017-05-03 17:15:52 fullCoverage: processing chromosome II
2017-05-03 17:15:52 loadCoverage: finding chromosome lengths
2017-05-03 17:15:52 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:15:55 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:15:59 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:16:02 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:16:05 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:16:09 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:16:11 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:16:11 filterData: normalizing coverage
2017-05-03 17:16:11 filterData: done normalizing coverage
2017-05-03 17:16:11 filterData: originally there were 813184 rows, now there are 813184 rows. Meaning that 0 percent was filtered.
2017-05-03 17:16:11 fullCoverage: processing chromosome III
2017-05-03 17:16:11 loadCoverage: finding chromosome lengths
2017-05-03 17:16:11 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:16:12 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:16:13 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:16:14 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:16:15 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:16:16 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:16:17 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:16:17 filterData: normalizing coverage
2017-05-03 17:16:17 filterData: done normalizing coverage
2017-05-03 17:16:17 filterData: originally there were 316620 rows, now there are 316620 rows. Meaning that 0 percent was filtered.
2017-05-03 17:16:17 fullCoverage: processing chromosome IV
2017-05-03 17:16:17 loadCoverage: finding chromosome lengths
2017-05-03 17:16:17 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:16:23 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:16:29 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:16:35 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:16:41 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:16:48 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:16:52 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:16:52 filterData: normalizing coverage
2017-05-03 17:16:53 filterData: done normalizing coverage
2017-05-03 17:16:53 filterData: originally there were 1531933 rows, now there are 1531933 rows. Meaning that 0 percent was filtered.
2017-05-03 17:16:53 fullCoverage: processing chromosome IX
2017-05-03 17:16:53 loadCoverage: finding chromosome lengths
2017-05-03 17:16:53 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:16:55 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:16:56 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:16:57 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:16:58 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:16:59 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:17:00 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:17:00 filterData: normalizing coverage
2017-05-03 17:17:00 filterData: done normalizing coverage
2017-05-03 17:17:00 filterData: originally there were 439888 rows, now there are 439888 rows. Meaning that 0 percent was filtered.
2017-05-03 17:17:00 fullCoverage: processing chromosome V
2017-05-03 17:17:00 loadCoverage: finding chromosome lengths
2017-05-03 17:17:00 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:17:02 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:17:05 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:17:07 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:17:10 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:17:13 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:17:15 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:17:15 filterData: normalizing coverage
2017-05-03 17:17:15 filterData: done normalizing coverage
2017-05-03 17:17:15 filterData: originally there were 576874 rows, now there are 576874 rows. Meaning that 0 percent was filtered.
2017-05-03 17:17:15 fullCoverage: processing chromosome VI
2017-05-03 17:17:15 loadCoverage: finding chromosome lengths
2017-05-03 17:17:15 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:17:16 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:17:17 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:17:18 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:17:19 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:17:20 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:17:20 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:17:20 filterData: normalizing coverage
2017-05-03 17:17:20 filterData: done normalizing coverage
2017-05-03 17:17:20 filterData: originally there were 270161 rows, now there are 270161 rows. Meaning that 0 percent was filtered.
2017-05-03 17:17:20 fullCoverage: processing chromosome VII
2017-05-03 17:17:21 loadCoverage: finding chromosome lengths
2017-05-03 17:17:21 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:17:25 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:17:28 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:17:32 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:17:36 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:17:40 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:17:43 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:17:43 filterData: normalizing coverage
2017-05-03 17:17:43 filterData: done normalizing coverage
2017-05-03 17:17:43 filterData: originally there were 1090940 rows, now there are 1090940 rows. Meaning that 0 percent was filtered.
2017-05-03 17:17:43 fullCoverage: processing chromosome VIII
2017-05-03 17:17:43 loadCoverage: finding chromosome lengths
2017-05-03 17:17:43 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:17:45 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:17:47 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:17:48 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:17:50 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:17:52 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:17:53 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:17:54 filterData: normalizing coverage
2017-05-03 17:17:54 filterData: done normalizing coverage
2017-05-03 17:17:54 filterData: originally there were 562643 rows, now there are 562643 rows. Meaning that 0 percent was filtered.
2017-05-03 17:17:54 fullCoverage: processing chromosome X
2017-05-03 17:17:54 loadCoverage: finding chromosome lengths
2017-05-03 17:17:54 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:17:56 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:17:59 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:18:01 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:18:03 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:18:06 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:18:07 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:18:07 filterData: normalizing coverage
2017-05-03 17:18:08 filterData: done normalizing coverage
2017-05-03 17:18:08 filterData: originally there were 745751 rows, now there are 745751 rows. Meaning that 0 percent was filtered.
2017-05-03 17:18:08 fullCoverage: processing chromosome XI
2017-05-03 17:18:08 loadCoverage: finding chromosome lengths
2017-05-03 17:18:08 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:18:10 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:18:11 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:18:13 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:18:15 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:18:17 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:18:18 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:18:18 filterData: normalizing coverage
2017-05-03 17:18:19 filterData: done normalizing coverage
2017-05-03 17:18:19 filterData: originally there were 666816 rows, now there are 666816 rows. Meaning that 0 percent was filtered.
2017-05-03 17:18:19 fullCoverage: processing chromosome XII
2017-05-03 17:18:19 loadCoverage: finding chromosome lengths
2017-05-03 17:18:19 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:18:26 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:18:34 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:18:42 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:18:48 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:18:56 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:18:59 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:18:59 filterData: normalizing coverage
2017-05-03 17:19:00 filterData: done normalizing coverage
2017-05-03 17:19:00 filterData: originally there were 1078177 rows, now there are 1078177 rows. Meaning that 0 percent was filtered.
2017-05-03 17:19:00 fullCoverage: processing chromosome XIII
2017-05-03 17:19:00 loadCoverage: finding chromosome lengths
2017-05-03 17:19:00 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:19:03 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:19:07 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:19:10 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:19:14 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:19:17 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:19:19 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:19:19 filterData: normalizing coverage
2017-05-03 17:19:20 filterData: done normalizing coverage
2017-05-03 17:19:20 filterData: originally there were 924431 rows, now there are 924431 rows. Meaning that 0 percent was filtered.
2017-05-03 17:19:20 fullCoverage: processing chromosome XIV
2017-05-03 17:19:20 loadCoverage: finding chromosome lengths
2017-05-03 17:19:20 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:19:23 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:19:26 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:19:28 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:19:31 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:19:34 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:19:36 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:19:36 filterData: normalizing coverage
2017-05-03 17:19:36 filterData: done normalizing coverage
2017-05-03 17:19:36 filterData: originally there were 784333 rows, now there are 784333 rows. Meaning that 0 percent was filtered.
2017-05-03 17:19:36 fullCoverage: processing chromosome XV
2017-05-03 17:19:36 loadCoverage: finding chromosome lengths
2017-05-03 17:19:36 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:19:41 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:19:45 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:19:49 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:19:53 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:19:58 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:20:01 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:20:01 filterData: normalizing coverage
2017-05-03 17:20:01 filterData: done normalizing coverage
2017-05-03 17:20:01 filterData: originally there were 1091291 rows, now there are 1091291 rows. Meaning that 0 percent was filtered.
2017-05-03 17:20:01 fullCoverage: processing chromosome XVI
2017-05-03 17:20:01 loadCoverage: finding chromosome lengths
2017-05-03 17:20:01 loadCoverage: loading BAM file /data/alignments/WT1/WT1Aligned.sorted.bam
2017-05-03 17:20:05 loadCoverage: loading BAM file /data/alignments/WT2/WT2Aligned.sorted.bam
2017-05-03 17:20:08 loadCoverage: loading BAM file /data/alignments/WT3/WT3Aligned.sorted.bam
2017-05-03 17:20:11 loadCoverage: loading BAM file /data/alignments/MT1/MT1Aligned.sorted.bam
2017-05-03 17:20:15 loadCoverage: loading BAM file /data/alignments/MT2/MT2Aligned.sorted.bam
2017-05-03 17:20:19 loadCoverage: loading BAM file /data/alignments/MT3/MT3Aligned.sorted.bam
2017-05-03 17:20:21 loadCoverage: applying the cutoff to the merged data
2017-05-03 17:20:21 filterData: normalizing coverage
2017-05-03 17:20:21 filterData: done normalizing coverage
2017-05-03 17:20:21 filterData: originally there were 948066 rows, now there are 948066 rows. Meaning that 0 percent was filtered.
extendedMapSeqlevels: the 'species' reallysaccharomyces_cerevisiaebutiwanttoseeifcangetregionmatrixtowork is currently not supported in GenomeInfoDb. Check valid 'species' by running names(GenomeInfoDb::genomeStyles()). If it's not present, consider adding your genome by following the information at http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf
user system elapsed
259.920 3.008 274.549
>
> system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75))
2017-05-03 17:22:36 regionMatrix: processing I
2017-05-03 17:22:36 filterData: originally there were 230218 rows, now there are 203924 rows. Meaning that 11.42 percent was filtered.
2017-05-03 17:22:36 findRegions: identifying potential segments
2017-05-03 17:22:36 findRegions: segmenting information
2017-05-03 17:22:36 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:36 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:36 getRegionCoverage: processing I
2017-05-03 17:22:36 getRegionCoverage: done processing I
2017-05-03 17:22:36 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:36 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:36 regionMatrix: processing II
2017-05-03 17:22:37 filterData: originally there were 813184 rows, now there are 760408 rows. Meaning that 6.48999999999999 percent was filtered.
2017-05-03 17:22:37 findRegions: identifying potential segments
2017-05-03 17:22:37 findRegions: segmenting information
2017-05-03 17:22:38 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:38 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:38 getRegionCoverage: processing II
2017-05-03 17:22:38 getRegionCoverage: done processing II
2017-05-03 17:22:38 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:39 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:39 regionMatrix: processing III
2017-05-03 17:22:39 filterData: originally there were 316620 rows, now there are 264390 rows. Meaning that 16.5 percent was filtered.
2017-05-03 17:22:39 findRegions: identifying potential segments
2017-05-03 17:22:39 findRegions: segmenting information
2017-05-03 17:22:39 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:39 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:39 getRegionCoverage: processing III
2017-05-03 17:22:39 getRegionCoverage: done processing III
2017-05-03 17:22:39 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:40 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:40 regionMatrix: processing IV
2017-05-03 17:22:41 filterData: originally there were 1531933 rows, now there are 1431824 rows. Meaning that 6.53 percent was filtered.
2017-05-03 17:22:41 findRegions: identifying potential segments
2017-05-03 17:22:41 findRegions: segmenting information
2017-05-03 17:22:42 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:42 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:42 getRegionCoverage: processing IV
2017-05-03 17:22:44 getRegionCoverage: done processing IV
2017-05-03 17:22:44 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:45 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:45 regionMatrix: processing IX
2017-05-03 17:22:45 filterData: originally there were 439888 rows, now there are 402936 rows. Meaning that 8.40000000000001 percent was filtered.
2017-05-03 17:22:45 findRegions: identifying potential segments
2017-05-03 17:22:45 findRegions: segmenting information
2017-05-03 17:22:45 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:45 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:45 getRegionCoverage: processing IX
2017-05-03 17:22:46 getRegionCoverage: done processing IX
2017-05-03 17:22:46 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:46 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:46 regionMatrix: processing V
2017-05-03 17:22:47 filterData: originally there were 576874 rows, now there are 533061 rows. Meaning that 7.59 percent was filtered.
2017-05-03 17:22:47 findRegions: identifying potential segments
2017-05-03 17:22:47 findRegions: segmenting information
2017-05-03 17:22:47 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:47 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:47 getRegionCoverage: processing V
2017-05-03 17:22:47 getRegionCoverage: done processing V
2017-05-03 17:22:47 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:48 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:48 regionMatrix: processing VI
2017-05-03 17:22:48 filterData: originally there were 270161 rows, now there are 243123 rows. Meaning that 10.01 percent was filtered.
2017-05-03 17:22:48 findRegions: identifying potential segments
2017-05-03 17:22:48 findRegions: segmenting information
2017-05-03 17:22:48 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:48 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:48 getRegionCoverage: processing VI
2017-05-03 17:22:48 getRegionCoverage: done processing VI
2017-05-03 17:22:48 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:48 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:48 regionMatrix: processing VII
2017-05-03 17:22:50 filterData: originally there were 1090940 rows, now there are 1002019 rows. Meaning that 8.15000000000001 percent was filtered.
2017-05-03 17:22:50 findRegions: identifying potential segments
2017-05-03 17:22:50 findRegions: segmenting information
2017-05-03 17:22:50 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:50 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:50 getRegionCoverage: processing VII
2017-05-03 17:22:51 getRegionCoverage: done processing VII
2017-05-03 17:22:51 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:52 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:52 regionMatrix: processing VIII
2017-05-03 17:22:52 filterData: originally there were 562643 rows, now there are 523276 rows. Meaning that 7 percent was filtered.
2017-05-03 17:22:52 findRegions: identifying potential segments
2017-05-03 17:22:52 findRegions: segmenting information
2017-05-03 17:22:52 findRegions: identifying candidate regions
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:52 findRegions: identifying region clusters
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
extendedMapSeqlevels: the current naming style could not be guessed. Consider supplying 'currentStyle'.
2017-05-03 17:22:53 getRegionCoverage: processing VIII
2017-05-03 17:22:53 getRegionCoverage: done processing VIII
2017-05-03 17:22:53 regionMatrix: calculating coverageMatrix
2017-05-03 17:22:53 regionMatrix: adjusting coverageMatrix for 'L'
2017-05-03 17:22:53 regionMatrix: processing X
2017-05-03 17:22:54 filterData: originally there were 745751 rows, now there are 696110 rows. Meaning that 6.66 percent was filtered.
2017-05-03 17:22:54 findRegions: identifying potential segments
2017-05-03 17:22:54 findRegions: segmenting information
2017-05-03 17:22:54 findRegions: identifying candidate regions
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2017-05-03 17:22:54 findRegions: identifying region clusters
Error in .normargSeqlengths(value, seqnames(x)) :
when the supplied 'seqlengths' vector is named, the names must match the seqnames
Timing stopped at: 18.168 0.468 18.64
> traceback()
14: stop(e)
13: value[[3L]](cond)
12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({
FUN(...)
}, error = handle_error)
9: withCallingHandlers({
tryCatch({
FUN(...)
}, error = handle_error)
}, warning = handle_warning)
8: FUN(X[[i]], ...)
7: lapply(X, FUN, ...)
6: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
.MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
5: bplapply(X = seq_along(ddd[[1L]]), wrap, .FUN = FUN, .ddd = ddd,
.MoreArgs = MoreArgs, BPREDO = BPREDO, BPPARAM = BPPARAM)
4: bpmapply(.regionMatrixByChr, fullCov, names(fullCov), MoreArgs = moreArgs,
SIMPLIFY = FALSE, BPPARAM = BPPARAM)
3: bpmapply(.regionMatrixByChr, fullCov, names(fullCov), MoreArgs = moreArgs,
SIMPLIFY = FALSE, BPPARAM = BPPARAM)
2: regionMatrix(fullCov, cutoff = 30, L = 75)
1: system.time(regionMat <- regionMatrix(fullCov, cutoff = 30, L = 75))
> session_info()
Session info -----------------------------------------------------------------------------------------------------------
setting value
version R version 3.3.1 (2016-06-21)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz <NA>
date 2017-05-03
Packages ---------------------------------------------------------------------------------------------------------------
package * version date source
acepack 1.4.1 2016-10-29 CRAN (R 3.3.1)
AnnotationDbi 1.36.2 2017-03-10 Bioconductor
backports 1.0.5 2017-01-18 CRAN (R 3.3.1)
base64enc 0.1-3 2015-07-28 CRAN (R 3.3.1)
Biobase 2.34.0 2017-03-10 Bioconductor
BiocGenerics * 0.20.0 2017-03-10 Bioconductor
BiocParallel 1.8.2 2017-05-01 Bioconductor
biomaRt 2.30.0 2017-03-10 Bioconductor
Biostrings 2.42.1 2017-03-10 Bioconductor
bitops 1.0-6 2013-08-17 CRAN (R 3.3.1)
BSgenome 1.42.0 2017-03-10 Bioconductor
bumphunter 1.14.0 2017-05-01 Bioconductor
checkmate 1.8.2 2016-11-02 CRAN (R 3.3.1)
cluster 2.0.6 2017-03-16 CRAN (R 3.3.1)
codetools 0.2-15 2016-10-05 CRAN (R 3.3.1)
colorspace 1.3-2 2016-12-14 CRAN (R 3.3.1)
data.table 1.10.4 2017-02-01 CRAN (R 3.3.1)
DBI 0.6-1 2017-04-01 CRAN (R 3.3.1)
derfinder * 1.8.5 2017-05-01 Bioconductor
derfinderHelper 1.8.1 2017-05-01 Bioconductor
devtools * 1.12.0 2016-12-05 CRAN (R 3.3.1)
digest 0.6.12 2017-01-27 CRAN (R 3.3.1)
doRNG 1.6.6 2017-04-10 CRAN (R 3.3.1)
foreach 1.4.3 2015-10-13 CRAN (R 3.3.1)
foreign 0.8-68 2017-04-24 CRAN (R 3.3.1)
Formula 1.2-1 2015-04-07 CRAN (R 3.3.1)
GenomeInfoDb * 1.10.3 2017-03-10 Bioconductor
GenomicAlignments 1.10.1 2017-05-01 Bioconductor
GenomicFeatures 1.26.4 2017-05-01 Bioconductor
GenomicFiles 1.10.3 2017-05-01 Bioconductor
GenomicRanges * 1.26.4 2017-05-01 Bioconductor
ggplot2 2.2.1 2016-12-30 CRAN (R 3.3.1)
gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.1)
gtable 0.2.0 2016-02-26 CRAN (R 3.3.1)
Hmisc 4.0-2 2016-12-31 CRAN (R 3.3.1)
htmlTable 1.9 2017-01-26 CRAN (R 3.3.1)
htmltools 0.3.6 2017-04-28 CRAN (R 3.3.1)
htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.1)
IRanges * 2.8.2 2017-05-01 Bioconductor
iterators 1.0.8 2015-10-13 CRAN (R 3.3.1)
knitr 1.15.1 2016-11-22 CRAN (R 3.3.1)
lattice 0.20-35 2017-03-25 CRAN (R 3.3.1)
latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.1)
lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.1)
locfit 1.5-9.1 2013-04-20 CRAN (R 3.3.1)
magrittr 1.5 2014-11-22 CRAN (R 3.3.1)
Matrix 1.2-10 2017-04-28 CRAN (R 3.3.1)
matrixStats 0.52.2 2017-04-14 CRAN (R 3.3.1)
memoise 1.1.0 2017-04-21 CRAN (R 3.3.1)
munsell 0.4.3 2016-02-13 CRAN (R 3.3.1)
nnet 7.3-12 2016-02-02 CRAN (R 3.3.1)
pkgmaker 0.22 2014-05-14 CRAN (R 3.3.1)
plyr 1.8.4 2016-06-08 CRAN (R 3.3.1)
qvalue 2.6.0 2017-05-01 Bioconductor
RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.1)
Rcpp 0.12.10 2017-03-19 CRAN (R 3.3.1)
RCurl 1.95-4.8 2016-03-01 CRAN (R 3.3.1)
registry 0.3 2015-07-08 CRAN (R 3.3.1)
reshape2 1.4.2 2016-10-22 CRAN (R 3.3.1)
rngtools 1.2.4 2014-03-06 CRAN (R 3.3.1)
rpart 4.1-11 2017-04-21 CRAN (R 3.3.1)
Rsamtools 1.26.2 2017-05-01 Bioconductor
RSQLite 1.1-2 2017-01-08 CRAN (R 3.3.1)
rstudioapi 0.6 2016-06-27 CRAN (R 3.3.1)
rtracklayer 1.34.2 2017-03-10 Bioconductor
S4Vectors * 0.12.2 2017-05-01 Bioconductor
scales 0.4.1 2016-11-09 CRAN (R 3.3.1)
stringi 1.1.5 2017-04-07 CRAN (R 3.3.1)
stringr 1.2.0 2017-02-18 CRAN (R 3.3.1)
SummarizedExperiment 1.4.0 2017-03-10 Bioconductor
survival 2.41-3 2017-04-04 CRAN (R 3.3.1)
tibble 1.3.0 2017-04-01 CRAN (R 3.3.1)
VariantAnnotation 1.20.3 2017-05-01 Bioconductor
withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
XML 3.98-1.6 2017-03-30 CRAN (R 3.3.1)
xtable 1.8-2 2016-02-05 CRAN (R 3.3.1)
XVector 0.14.1 2017-05-01 Bioconductor
zlibbioc 1.20.0 2017-03-10 Bioconductor
>
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