[BioC] pileupAsGRanges hangs
Martin Morgan
mtmorgan at fhcrc.org
Mon Dec 10 17:27:46 CET 2012
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 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 666686;;;66;666;;;;=;6666;;66;6;666;6;36;6A6;=;63;;;666363=;;66;6;86;6=6;633=;666=66A68;;;;;=86;
> chr8 13167122 N 96 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTT 777777747377337788787(777477773777778837748777773777377383877377378772877*337777787373782747-777
> chr8 13167123 N 96 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 88881888:888888718888888=888888888888888:88888888888888888888888888888888888=8=88888=88=88888888
> chr8 13167124 N 96 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT <=@=:<<;<=><==<::><<;><<=<<7><=<<<@<>;=<<<><<><==<;<=<<<7=<=<><;<<<=<:<=<;==<<<;=>==<<<=<<:<;><=
> chr8 13167125 N 96 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCC 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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAA 2:::-:)9:=::==44:6:::::6::::::=::-::::=:::84:8)==:::=::::===9:2::::=+92*86==:84=:5:=4;8:*468884=
> chr8 13167127 N 96 TTTTTTTTTTTTTT-1NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT;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*GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG <<<<<<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
>
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