[BioC] exomeCopy - memory error

[love]

Hi Francesco,

I'm not sure about the source of this error.

You could try to isolate the error by testing if you can extract a very
simple set of reads from the BAM file using scanBam from the Rsamtools
package.

something like:

some.reads <- scanBam(bam.file, param=ScanBamParam(what=c("pos","mapq"),
which=GRanges("chr1",IRanges(1,1000000))))

best,

Mike

> From: Lescai, Francesco <f.lescai at ucl.ac.uk>
> Date: Tue, Sep 18, 2012 at 4:43 PM
> Subject: [BioC] exomeCopy - memory error
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> 
> 
> Hi there,
> I'm encountering a memory error with exomeCopy which might be
file-specific
> (i.e. it's not happening with any of my other batches).
> I'm running it on a cluster.
> 
> Initially I had three batches pooled together and I had this error
message
> in my .Rout file
> 
> ----------------
>> for (f1 in bamfiles){
> +  sample<-gsub('.bam','',f1)
> +  exome.samples<-c(exome.samples,sample)
> +  rdata[[sample]] <- countBamInGRanges(f1,target.sub)
> + }
> Error in value[[3L]](cond) :
>   Realloc could not re-allocate memory (20971520 bytes)
>   file: /SAN/biomed/biomed14/ICH2/k/bam_batch_3/K_5165129.bam
>   index: /SAN/biomed/biomed14/ICH2/k/bam_batch_3/K_5165129.bam
> Calls: countBamInGRanges ... tryCatch -> tryCatchList -> tryCatchOne ->
> <Anonymous>
> Execution halted
> ------------------
> 
> The index doesn't seem to point to a .bam.bai file, but I checked of
course
> and the .bai is there, same way as for the other bams I'm counting in.
> Then I separated the batches, and run again.
> Two of three didn't display any error,  while the third one (the one
that
> .bam file belongs to) had this (slightly different) error
> 
> -------------------------
>> for (f1 in bamfiles){
> +  sample<-gsub('.bam','',f1)
> +  exome.samples<-c(exome.samples,sample)
> +  rdata[[sample]] <- countBamInGRanges(f1,target.sub)
> + }
> 
>  *** caught segfault ***
> address 0x4, cause 'memory not mapped'
> 
> Traceback:
>  1: .Call(.bamfile_open, path(con), index(con), "rb")
>  2: open.BamFile(BamFile(file, index), "rb")
>  3: open(BamFile(file, index), "rb")
>  4: scanBam(bam.file, param = ScanBamParam(what = scan.what, which =
> range(granges.subset)))
>  5: scanBam(bam.file, param = ScanBamParam(what = scan.what, which =
> range(granges.subset)))
>  6: countBamInGRanges(f1, target.sub)
> aborting ...
> -------------------------
> 
> Any idea where I could look better, in order to track this error?
> 
> thanks for your help,
> Francesco
> 
> 
> 
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>  [7] LC_PAPER=C                     LC_NAME=C
>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] exomeCopy_1.2.0     Rsamtools_1.8.5     Biostrings_2.24.1
> [4] GenomicRanges_1.8.7 IRanges_1.14.4      BiocGenerics_0.2.0
> 
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 stats4_2.15.0  zlibbioc_1.2.0
> 
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