[Bioc-devel] scanBam() segfault error

4 messages · Martin Morgan, Leonard Goldstein

Original

1

4

Leonard Goldstein

Fri, Apr 17, 2015 8:59 AM #

Hi all,

I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for
your help.

Leonard

R Under development (unstable) (2014-11-04 r66932)
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=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] Rsamtools_1.19.54     Biostrings_2.35.13    XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20   IRanges_2.1.45
[7] S4Vectors_0.5.23      BiocGenerics_0.13.11

loaded via a namespace (and not attached):
[1] bitops_1.0-6    compiler_3.2.0  tools_3.2.0     zlibbioc_1.13.3

*** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'

Traceback:
 1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter,     ...)
 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,
tagFilter,         ...)}, error = function(err) {
stop(conditionMessage(err), "\n  f\
ile: ", path(file), "\n  index: ",         index(file))})
 6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
  tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
 7: scanBam(file = file, param = param)
 8: scanBam(file = file, param = param)

Fri, Apr 17, 2015 9:12 AM #

On 04/17/2015 08:59 AM, Leonard Goldstein wrote:

Probably a BAM file would be a big help... Thanks, Martin

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

3 days later

Mon, Apr 20, 2015 10:59 AM #

On 04/17/2015 09:12 AM, Martin Morgan wrote:

Thanks Leonard, I think this is addressed in 1.20.1 / 1.21.1, which are not yet 
available via biocLite.

I will likely revisit this code in the next week or so; please let me know if 
there are other issues.

Martin

your help.

Leonard

sessionInfo()

R Under development (unstable) (2014-11-04 r66932)
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=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] Rsamtools_1.19.54     Biostrings_2.35.13    XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20   IRanges_2.1.45
[7] S4Vectors_0.5.23      BiocGenerics_0.13.11

loaded via a namespace (and not attached):
[1] bitops_1.0-6    compiler_3.2.0  tools_3.2.0     zlibbioc_1.13.3

gr <- GRanges("16", IRanges(13173149, 15234449), "+")

file <- BamFile(file, asMates = TRUE)

param <- ScanBamParam(what = scanBamWhat(), which = gr)

tmp <- scanBam(file = file, param = param)

  *** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'

Traceback:
  1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter,     ...)
  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,
tagFilter,         ...)}, error = function(err) {
stop(conditionMessage(err), "\n  f\
ile: ", path(file), "\n  index: ",         index(file))})
  6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
   tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
  7: scanBam(file = file, param = param)
  8: scanBam(file = file, param = param)

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

Leonard Goldstein

Mon, Apr 20, 2015 2:30 PM #

Thanks Martin. I had one other test case that resulted in a segfault.
I just tried Rsamtools 1.21.1 and both cases work fine with the new
version. Thanks for your help and for fixing this so quickly.

Leonard

On Mon, Apr 20, 2015 at 10:59 AM, Martin Morgan <mtmorgan at fredhutch.org> wrote:

On 04/17/2015 09:12 AM, Martin Morgan wrote:

On 04/17/2015 08:59 AM, Leonard Goldstein wrote:

Hi all,

I ran into a segfault error when trying to read paired-end RNA-seq
alignments with scanBam (see below). This seems to be a problem
introduced in Rsamtools version 1.19.35 (1.19.34 works fine). In case
you need the BAM file for testing, please let me know. Many thanks for


Probably a BAM file would be a big help... Thanks, Martin


Thanks Leonard, I think this is addressed in 1.20.1 / 1.21.1, which are not
yet available via biocLite.

I will likely revisit this code in the next week or so; please let me know
if there are other issues.


Martin

your help.

Leonard

sessionInfo()

R Under development (unstable) (2014-11-04 r66932)
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=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] Rsamtools_1.19.54     Biostrings_2.35.13    XVector_0.7.4
[4] GenomicRanges_1.19.57 GenomeInfoDb_1.3.20   IRanges_2.1.45
[7] S4Vectors_0.5.23      BiocGenerics_0.13.11

loaded via a namespace (and not attached):
[1] bitops_1.0-6    compiler_3.2.0  tools_3.2.0     zlibbioc_1.13.3


gr <- GRanges("16", IRanges(13173149, 15234449), "+")

file <- BamFile(file, asMates = TRUE)

param <- ScanBamParam(what = scanBamWhat(), which = gr)

tmp <- scanBam(file = file, param = param)


  *** caught segfault ***
address 0x14538b1e, cause 'memory not mapped'

Traceback:
  1: .Call(func, .extptr(file), space, flag, simpleCigar, tagFilter,
...)
  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,
tagFilter,         ...)}, error = function(err) {
stop(conditionMessage(err), "\n  f\
ile: ", path(file), "\n  index: ",         index(file))})
  6: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
   tmpl, obeyQname(file), asMates(file), qnamePrefix, qnameSuffix,
param = param)
  7: scanBam(file = file, param = param)
  8: scanBam(file = file, param = param)

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel