Question: yieldSize and paired end data in SummarizeOverlaps error?
6.5 years ago by
Thomas Whisenant • 10
Thomas Whisenant • 10 wrote:
Hello all, I am attempting to use summarizeOverlaps to assign counts to exons using paired end Tophat alignments. As an example, I have created a bamfilelist containing one bamfile and a feature list of exons by gene. This is followed by using summarizeOverlaps with the single end parameter set to false. bfl <- BamFileList("EP04.bam", index="EP04.bam", yieldSize=1000000) exons.by.gene <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene") all.exons <- unlist(exons.by.gene) sumexp <- summarizeOverlaps( features=all.exons, reads=bfl, mode=IntersectionNotEmpty, singleEnd=FALSE, ignore.strand=TRUE, parallel=TRUE) Error: cannot allocate vector of size 277.9 Mb In addition: Warning message: In readBamGappedAlignmentPairs(bf, param = param) : 'yieldSize' set to 'NA' Even with the parallel option, this process uses all available memory which presumably leads to the vector allocation error. While I have set the yieldSize in the BamFileList, this parameter does not appear to be used. Running summarizeOverlaps with "singleEnd=TRUE" does not issue a yieldSize warning. Any ideas on how to get set the yieldSize with "singleEnd=FALSE"? Thanks, Tom R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  DEXSeq_1.4.0  Rsamtools_1.10.2  org.Hs.eg.db_2.8.0  RSQLite_0.11.2  DBI_0.2-5  TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0  GenomicFeatures_1.10.1  BSgenome.Hsapiens.UCSC.hg19_1.3.19  BSgenome_1.26.1  Biostrings_2.26.3  GenomicRanges_1.10.6  IRanges_1.16.5  annotate_1.36.0  AnnotationDbi_1.20.3  Biobase_2.18.0  BiocGenerics_0.4.0 loaded via a namespace (and not attached):  biomaRt_2.14.0 bitops_1.0-5 hwriter_1.3  RCurl_1.95-3 rtracklayer_1.18.2 statmod_1.4.17  stats4_2.15.2 stringr_0.6.2 tools_2.15.2  XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 Thomas Whisenant, Ph.D. Salomon Lab, MEM-241 Department of Molecular and Experimental Medicine The Scripps Research Institute 10550 North Torrey Pines Rd. La Jolla, CA 92037 firstname.lastname@example.org<mailto:email@example.com> [[alternative HTML version deleted]]
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