Hi Martin, Yes, I was using the code in biovizBase. I upgraded as suggested, and it seems to work now. Many thanks. Mark On Mon, Dec 10, 2012 at 4:27 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 12/10/2012 05:03 PM, Mark Dunning wrote: >> >> Hi, >> >> I'm trying to generate some pileups from targetted-resequence data, >> but finding that the pileupAsGRanges command just hangs on some bam >> file and region combinations. The following works fine; > > > There was a bug like this fixed in Rsamtools 1.9.17, so a solution might be > to upgrade to the current release > > source("http://bioconductor.org/biocLite.R") > biocLite("BiocUpgrade") > > You might be able to narrow this to the Rsamtools::applyPileups code vs. > code from biovizBase (where I'm guessing pileupAsGRanges is coming from?) by > invoking > > pileupFiles <- PileupFiles(bams) > pileupParams <- PileupParam(which = gr, ...) > applyPileups(pileupFiles, function(...) NULL, param=pileupParams) > > If it is applyPileups, and it is not fixed in the current release, then it > would be great if you could send me a small bam file (e.g., using filterBam > to select the problem region). > > Martin > > >> >> >> gr <- ampRng[j,] >>> >>> gr >> >> GRanges with 1 range and 1 elementMetadata col: >> seqnames ranges strand | Symbol >> <rle> <iranges> <rle> | <factor> >> amp11 chr8 [13167119, 13167317] * | Lamp1 >> --- >> seqlengths: >> chr1 chr10 chr11 chr18 chr2 chr3 chr4 chr6 chr8 >> NA NA NA NA NA NA NA NA NA >> >> >> bam <- "CleanedBams/2424-N1-2.bam" >> pu <- pileupAsGRanges(bam, region=gr) >> >>> head(pu) >> >> GRanges with 6 ranges and 7 elementMetadata cols: >> seqnames ranges strand | A C >> G >> <rle> <iranges> <rle> | <integer> <integer> >> <integer> >> [1] chr8 [13167119, 13167119] + | 0 176 >> 0 >> [2] chr8 [13167120, 13167120] + | 0 206 >> 0 >> [3] chr8 [13167121, 13167121] + | 0 1 >> 0 >> [4] chr8 [13167122, 13167122] + | 0 0 >> 0 >> [5] chr8 [13167123, 13167123] + | 0 251 >> 0 >> [6] chr8 [13167124, 13167124] + | 0 3 >> 0 >> T N depth bam >> <integer> <integer> <numeric> <character> >> [1] 1 0 177 CleanedBams/2424-N1-2.bam >> [2] 0 0 206 CleanedBams/2424-N1-2.bam >> [3] 248 0 249 CleanedBams/2424-N1-2.bam >> [4] 251 0 251 CleanedBams/2424-N1-2.bam >> [5] 2 0 253 CleanedBams/2424-N1-2.bam >> [6] 251 0 254 CleanedBams/2424-N1-2.bam >> --- >> seqlengths: >> chr8 >> NA >> >> But if I try and get the pileup of the same region, but a different >> bam file, R just hangs forever and never produces any output. Nor does >> it give me an error message so I'm not sure what it's actually doing. >> >>> bam <- "CleanedBams/2424-N1-1.bam" >> >> >>> pu <- pileupAsGRanges(bam, region=gr) >> >> >> >> Any idea how I can debug the problem.? I am able to run samtools >> pileup at the command line for the offending bam file without any >> problem. >> >> >> samtools mpileup -r chr8:13167119-13167317 CleanedBams/2424-N1-1.bam | >> head >> >> [mpileup] 1 samples in 1 input files >> <mpileup> Set max per-file depth to 8000 >> chr8 13167119 N 96 >> ^>C^]C^>C^>C^>C^2C^]C^>C^2T^>C^]C^>C^]C^]C^>C^>C^>T^]C^>C^>C^>C^>C^ >C^>C^]C^>C^>C^>C^>C^]C^]C^]C^>C^2C^>C^>C^]C^>C^]C^>C^]C^]C^>C^>C^>C^> T^>C^]T^]C^>C^]C^>C^]C^]C^]C^]C^]C^>C^]T^>T^>C^]C^]C^]C^]C^>T^>C^>C^>C ^>C^>C^]C^>T^>C^]C^]C^]T^]C^]C^]C^]C^]C^>C^]C^>C^>C^>C^]C^2T^>C^>C^>C^ ]C^>C^]C^]T >> )$.,),*.$,)$-,.)$)-)--,.,.,,-,,,,,*.,.,,..$)-$-$,-$.,,,,,+$$$,,.,$$ ,$...*-++$$-..-,+),-*$-$..$-$ >> chr8 13167120 N 96 >> CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCC >> -0++0+0-6+-0-+--;-.2-+*++**-+*+*++-*+9)+++--06.1+--9+++++);;0++++10 +0.9+6-));0+-+2*)2-02120-.0-6 >> chr8 13167121 N 96 >> TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTT >> 666686;;;66;666;;;;=;6666;;66;6;666;6;36;6A6;=;63;;;666363=;;66;6;8 6;6=6;633=;666=66A68;;;;;=86; >> chr8 13167122 N 96 >> TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTCTTTTTTTTTTTTTTTTTTTTTT >> 777777747377337788787(777477773777778837748777773777377383877377378 772877*337777787373782747-777 >> chr8 13167123 N 96 >> CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCCCCCCCCCCC >> 88881888:888888718888888=888888888888888:88888888888888888888888888 888888888=8=88888=88=88888888 >> chr8 13167124 N 96 >> TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTT >> <=@=:<<;<=><==<::><<;><<=<<7><=<<<@<>;=<<<><<><==<;<=<<<7=<=<><;<<< =<:<=<;==<<<;=>==<<<=<<:<;><= >> chr8 13167125 N 96 >> CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CACCCCCCCCCCCCCCCCCCCCCCCCCCC >> 9<:<78:::;:0;:::86:73::6;5:38:::::;;:8;:8:8:7:9;;:35;:79:;:::::8;:6 ;93:;:8;;7:8:;8:;3::97:8383<; >> chr8 13167126 N 96 >> AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAGAAAAAAAAAAAAAA >> 2:::-:)9:=::==44:6:::::6::::::=::-::::=:::84:8)==:::=::::===9:2:::: =+92*86==:84=:5:=4;8:*468884= >> chr8 13167127 N 96 >> TTTTTTTTTTTTTT-1NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;9<9=.95<>>89<..>9>>>;:><9<<;9899<8;;< 8><99.8<59999>9<9:99:9<9;99:99:<<:;;98><;<9>9959>;.<:==:>9 >> chr8 13167128 N 96 >> GGGGGGGGGGGGG*GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG GGGGGGGGGGGGGGGGGGGGGGGGGGGGG >> <<<<<<8-<<<8<<6<4-;<;<<<;<<<:<<<<6<<6;<6<<6<;<<<<<<<:6<<47<<<<<<<<6 <8;<<<-<<<<8<<::<6<<6<<<<86;< >> >> >> Regards, >> >> Mark >> >> >>> sessionInfo() >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biovizBase_1.4.2 Rsamtools_1.8.6 Biostrings_2.24.1 >> [4] GenomicRanges_1.8.13 IRanges_1.14.4 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.18.3 Biobase_2.16.0 biomaRt_2.12.0 >> [4] bitops_1.0-4.1 BSgenome_1.24.0 cluster_1.14.2 >> [7] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4 >> [10] GenomicFeatures_1.8.3 grid_2.15.1 Hmisc_3.9-3 >> [13] labeling_0.1 lattice_0.20-10 munsell_0.4 >> [16] plyr_1.7.1 RColorBrewer_1.0-5 RCurl_1.91-1 >> [19] RSQLite_0.11.2 rtracklayer_1.16.3 scales_0.2.2 >> [22] stats4_2.15.1 stringr_0.6.1 tools_2.15.1 >> [25] XML_3.9-4 zlibbioc_1.2.0 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793