[BioC] pileupAsGRanges hangs
Mark Dunning
mark.dunning at gmail.com
Tue Dec 11 10:40:23 CET 2012
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
>> 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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>
>
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