[BioC] pileupAsGRanges hangs

Mon Dec 10 17:03:41 CET 2012

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;

	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