[Bioc-sig-seq] scanBam segfault

[Martin Morgan]

On 07/14/2011 01:11 PM, Ivan Gregoretti wrote:
> Hello everybody,
>
> scanBam() is reporting segfaults. I tried in two different machines,
> with identical error reports.
>
> Actually, I have four BAM files from which I am only reading in the
> oligo sequences, nothing else. Two of them load fine but the other two
> produce the error.
>
> Loading fine: BAMs with 70887462 and 58162986 records
> Loading with segfault: BAMs with 101611824 and 114530023
>
> So, smaller are fine, bigger just crash.
>
> Do you guys run into the same problem?

I don't have immediate access to HiSeq bam files; are there any publicly 
available?

Also, it would help to have a C-level backtrace, maybe by doing

   R -d gdb -f test.R

where test.R contains a basic script to reproduce the crash. You'll end 
up at the gdb prompt. Type 'r' to run

   gdb> r

and then when the segfault occurs

   gdb> bt

to generate the back trace (maybe several screens). If you could forward 
that to me, on or off list, that would be a better starting point.

Martin
>
> Thank you,
>
> Ivan
>
> *****************************************************************
>
>> filebam<- "/home/igregore/my/data3/runs/110705/Project_81BRRABXX/c466.bam"
>> filebai<- "/home/igregore/my/data3/runs/110705/Project_81BRRABXX/c466"
>> param<- ScanBamParam(what = c("seq"))
>> myheader<- scanBamHeader(file=filebam)
>> c466Ba<- scanBam(file=filebam, index=filebai, param=param)
>
>   *** caught segfault ***
> address 0x7fb9a9773030, cause 'memory not mapped'
>
> Traceback:
>   1: .Call(func, .extptr(file), space, flag, simpleCigar, ...)
>   2: doTryCatch(return(expr), name, parentenv, handler)
>   3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
>   4: tryCatchList(expr, classes, parentenv, handlers)
>   5: tryCatch({    .Call(func, .extptr(file), space, flag, simpleCigar,
> ...)}, error = function(err) {    stop(conditionMessage(err), "\n
> file: ", path(file), "\n  index: ",         index(file))})
>   6: .io_bam(.scan_bamfile, file, param = param, path(file),
> index(file),     "rb", reverseComplement, tmpl)
>   7: scanBam(bam, param = param)
>   8: scanBam(bam, param = param)
>   9: eval(expr, envir, enclos)
> 10: eval(call, sys.frame(sys.parent()))
> 11: callGeneric(bam, ..., param = param)
> 12: scanBam(file = filebam, index = filebai, param = param)
> 13: scanBam(file = filebam, index = filebai, param = param)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
> ***********************************************************************
>> sessionInfo()
> R version 2.14.0 Under development (unstable) (2011-04-14 r55450)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.11.26    latticeExtra_0.6-18  RColorBrewer_1.0-5
> [4] lattice_0.19-30      Rsamtools_1.5.38     Biostrings_2.21.6
> [7] GenomicRanges_1.5.16 IRanges_1.11.11
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.13.7 grid_2.14.0    hwriter_1.3    zlibbioc_0.1.7
>
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