[BioC] exomeCopy - memory error

[love]

hi Francesco,

I'm not sure how you might get around these errors, but if you continue to
have trouble with these BAM files, you can try counting reads using
summarizeOverlaps in the GenomicRanges package, or counting reads outside
of R and then importing these counts (options here: generate a SAM file and
use htseq-count
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count or use
BEDTools coverage with -abam and -counts.)

cheers,

Mike

-------- Original Message --------
From: Lescai, Francesco <f.lescai at ucl.ac.uk>
Date: Wed, Sep 19, 2012 at 2:19 PM
Subject: Re: [BioC] exomeCopy - memory error
To: Martin Morgan <mtmorgan at fhcrc.org>
Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>


Thanks Mike and Martin for your advice.

>From within the script, the .Rout didn't report the file name in the
second case.
It turned out to be two different errors in two different files, which I
identified using the trace you suggested.
Other files don't give that problem.

Below my tests and the output: I cut repeated text, but it's still quite
long. My apologies for that.
I run Picard ValidateSam on several files.
there are a few errors of this kind

ERROR: Record 57116264, Read name HS16_6904:5:1203:11452:139702#8, MAPQ
should be 0 for unmapped read.

with the only difference that the file kc5165129.bam generating the
"Realloc" error has a bit more of those, compared to the one generating a
segmentation fault.
these few errors shouldn't be the problem however, because they are
present
also in the files which run smoothly.

thanks,
Francesco

-------------------------

Any idea where I could look better, in order to track this error?

but this looks like a different error, unrelated to memory allocation.
Mike's suggestion to narrow it to invoking essentially step 3 in the
traceback -- open(BamFile(file, index), "rb") -- is the best way forward.
To get there, you might say

 trace(scanBam, quote({ print(file); print(param) }))

to figure out where in countBamInGRanges() things are going wrong.

Martin




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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--
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


---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai at ucl.ac.uk<mailto:f.lescai at ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
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