[Bioc-sig-seq] scanBam segfault

[Ivan Gregoretti]

Thank you.

Ivan


On Sat, Jul 16, 2011 at 9:20 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 07/15/2011 02:40 AM, Martin Morgan wrote:
>>
>> 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.
>
> The segfault is fixed in Rsamtools 1.5.39; the bug was introduced in 1.5.35.
> Thanks for the report.
>
> Martin
>
>>>
>>> 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
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>
>
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