'Rsamtools' produces segfaults with XS tag
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@andrew-tikhonov-4215
Last seen 9.6 years ago
Dear Biocore Team, We've got a problem where 'Rsamtools' produces segfaults and core- dumps when reading a .bam file using the "XS" tag. We have a faulty .bam and the list or R commands to reproduce it. Could you please point us to someone who we may discuss this matter with and, if possible, fix the problem. Thanks a lot in advance. Regards, Andrew
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@martin-morgan-1513
Last seen 6 weeks ago
United States
Thanks Misha for the additional hints; I looked at the code and couldn't see anything immediately wrong, but if you can provide a (minimal?) bam file displaying the problem that would be helpful. Martin Misha Kapushesky <ostolop at="" ebi.ac.uk=""> writes: > Hi, > > I can add more detail to this - the same problem: > >> library( "Rsamtools" ) > ... >> tags <- c("NM", "MD", "XA", "XS","NS") >> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" >> and_bam = scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) > > *** caught segfault *** > address 0x2b3449beb8cd, cause 'invalid permissions' > > Traceback: > 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) > 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) > 3: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) > 4: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) > > This error goes away if we don't include "XS" in tags, also if we use > version 1.0.0 of Rsamtools. Any ideas? > > The sessionInfo() output is below. Thanks in advance! > > --Misha > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-unknown-linux-gnu > > locale: > [1] C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 > [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 > [7] rJava_0.8-4 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 > > > On Thu, 12 Aug 2010, Andrew Tikhonov wrote: > >> Dear Biocore Team, >> >> We've got a problem where 'Rsamtools' produces segfaults and >> core-dumps when reading a .bam file using the "XS" tag. We have a >> faulty .bam and the list or R commands to reproduce it. Could you >> please point us to someone who we may discuss this matter with and, >> if possible, fix the problem. >> >> Thanks a lot in advance. >> >> Regards, >> Andrew >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan 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
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Hi, I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. After some more tinkering - it seems I can't reproduce this on my Mac, only on our Linux install. I also just noticed that the released version is 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps it's a version incompatibility and we managed to install ourselves something incompatible? If that's the case, we'll probably try to get a more standard install going, and hopefully the problem will go away... --Misha On Fri, 13 Aug 2010, Martin Morgan wrote: > Thanks Misha for the additional hints; I looked at the code and couldn't > see anything immediately wrong, but if you can provide a (minimal?) bam > file displaying the problem that would be helpful. Martin > > Misha Kapushesky <ostolop at="" ebi.ac.uk=""> writes: > >> Hi, >> >> I can add more detail to this - the same problem: >> >>> library( "Rsamtools" ) >> ... >>> tags <- c("NM", "MD", "XA", "XS","NS") >>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" >>> and_bam = scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >> >> *** caught segfault *** >> address 0x2b3449beb8cd, cause 'invalid permissions' >> >> Traceback: >> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) >> 3: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >> 4: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >> >> This error goes away if we don't include "XS" in tags, also if we use >> version 1.0.0 of Rsamtools. Any ideas? >> >> The sessionInfo() output is below. Thanks in advance! >> >> --Misha >> >>> sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-unknown-linux-gnu >> >> locale: >> [1] C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 >> [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 >> [7] rJava_0.8-4 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.8.0 >> >> >> On Thu, 12 Aug 2010, Andrew Tikhonov wrote: >> >>> Dear Biocore Team, >>> >>> We've got a problem where 'Rsamtools' produces segfaults and >>> core-dumps when reading a .bam file using the "XS" tag. We have a >>> faulty .bam and the list or R commands to reproduce it. Could you >>> please point us to someone who we may discuss this matter with and, >>> if possible, fix the problem. >>> >>> Thanks a lot in advance. >>> >>> Regards, >>> Andrew >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Martin Morgan > 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 >
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On 8/13/2010 2:11 PM, Misha Kapushesky wrote: > Hi, > > I put it on > http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. After > some more tinkering - it seems I can't reproduce this on my Mac, only > on our Linux install. I also just noticed that the released version is > 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps > it's a version incompatibility and we managed to install ourselves > something incompatible? If that's the case, we'll probably try to get > a more standard install going, and hopefully the problem will go away... > This should be fixed in 1.0.8 (release) or 1.1.12 (devel), available via biocLite in the next several days or via svn (http://bioconductor.org/developers/source-control/) immediately. Thanks for the report and sample data. Martin > --Misha > > On Fri, 13 Aug 2010, Martin Morgan wrote: > >> Thanks Misha for the additional hints; I looked at the code and couldn't >> see anything immediately wrong, but if you can provide a (minimal?) bam >> file displaying the problem that would be helpful. Martin >> >> Misha Kapushesky <ostolop at="" ebi.ac.uk=""> writes: >> >>> Hi, >>> >>> I can add more detail to this - the same problem: >>> >>>> library( "Rsamtools" ) >>> ... >>>> tags <- c("NM", "MD", "XA", "XS","NS") >>>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" >>>> and_bam = scanBam(and_file, param = ScanBamParam(flag = >>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>> >>> *** caught segfault *** >>> address 0x2b3449beb8cd, cause 'invalid permissions' >>> >>> Traceback: >>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >>> param) >>> 3: scanBam(and_file, param = ScanBamParam(flag = >>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>> 4: scanBam(and_file, param = ScanBamParam(flag = >>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>> >>> This error goes away if we don't include "XS" in tags, also if we use >>> version 1.0.0 of Rsamtools. Any ideas? >>> >>> The sessionInfo() output is below. Thanks in advance! >>> >>> --Misha >>> >>>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] tools stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 >>> [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 >>> [7] rJava_0.8-4 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.8.0 >>> >>> >>> On Thu, 12 Aug 2010, Andrew Tikhonov wrote: >>> >>>> Dear Biocore Team, >>>> >>>> We've got a problem where 'Rsamtools' produces segfaults and >>>> core-dumps when reading a .bam file using the "XS" tag. We have a >>>> faulty .bam and the list or R commands to reproduce it. Could you >>>> please point us to someone who we may discuss this matter with and, >>>> if possible, fix the problem. >>>> >>>> Thanks a lot in advance. >>>> >>>> Regards, >>>> Andrew >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> Martin Morgan >> 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 >>
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Hi, Thanks for the speedy fix! --Misha On Fri, 13 Aug 2010, Martin Morgan wrote: > On 8/13/2010 2:11 PM, Misha Kapushesky wrote: >> Hi, >> >> I put it on http://www.ebi.ac.uk/~ostolop/accepted_hits.sortednames.bam. >> After some more tinkering - it seems I can't reproduce this on my Mac, only >> on our Linux install. I also just noticed that the released version is >> 1.0.7, while we seem to have 1.1.11, and yet our R is 2.11.1 - perhaps it's >> a version incompatibility and we managed to install ourselves something >> incompatible? If that's the case, we'll probably try to get a more standard >> install going, and hopefully the problem will go away... >> > > This should be fixed in 1.0.8 (release) or 1.1.12 (devel), available via > biocLite in the next several days or via svn > (http://bioconductor.org/developers/source-control/) immediately. > > Thanks for the report and sample data. > > Martin > >> --Misha >> >> On Fri, 13 Aug 2010, Martin Morgan wrote: >> >>> Thanks Misha for the additional hints; I looked at the code and couldn't >>> see anything immediately wrong, but if you can provide a (minimal?) bam >>> file displaying the problem that would be helpful. Martin >>> >>> Misha Kapushesky <ostolop at="" ebi.ac.uk=""> writes: >>> >>>> Hi, >>>> >>>> I can add more detail to this - the same problem: >>>> >>>>> library( "Rsamtools" ) >>>> ... >>>>> tags <- c("NM", "MD", "XA", "XS","NS") >>>>> and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" >>>>> and_bam = scanBam(and_file, param = ScanBamParam(flag = >>>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> >>>> *** caught segfault *** >>>> address 0x2b3449beb8cd, cause 'invalid permissions' >>>> >>>> Traceback: >>>> 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) >>>> 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = >>>> param) >>>> 3: scanBam(and_file, param = ScanBamParam(flag = >>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> 4: scanBam(and_file, param = ScanBamParam(flag = >>>> scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) >>>> >>>> This error goes away if we don't include "XS" in tags, also if we use >>>> version 1.0.0 of Rsamtools. Any ideas? >>>> >>>> The sessionInfo() output is below. Thanks in advance! >>>> >>>> --Misha >>>> >>>>> sessionInfo() >>>> R version 2.11.1 (2010-05-31) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 >>>> [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 >>>> [7] rJava_0.8-4 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] Biobase_2.8.0 >>>> >>>> >>>> On Thu, 12 Aug 2010, Andrew Tikhonov wrote: >>>> >>>>> Dear Biocore Team, >>>>> >>>>> We've got a problem where 'Rsamtools' produces segfaults and >>>>> core-dumps when reading a .bam file using the "XS" tag. We have a >>>>> faulty .bam and the list or R commands to reproduce it. Could you >>>>> please point us to someone who we may discuss this matter with and, >>>>> if possible, fix the problem. >>>>> >>>>> Thanks a lot in advance. >>>>> >>>>> Regards, >>>>> Andrew >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> Martin Morgan >>> 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 >>> >
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@misha-kapushesky-1334
Last seen 9.6 years ago
Hi, I can add more detail to this - the same problem: > library( "Rsamtools" ) ... > tags <- c("NM", "MD", "XA", "XS","NS") > and_file = "SRR034792/tophat_out/accepted_hits.sortednames.bam" > and_bam = scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) *** caught segfault *** address 0x2b3449beb8cd, cause 'invalid permissions' Traceback: 1: .Call(func, file, index, "rb", NULL, flag, simpleCigar, ...) 2: .io_bam(.scan_bam, file, index, reverseComplement, tmpl, param = param) 3: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) 4: scanBam(and_file, param = ScanBamParam(flag = scanBamFlag(isUnmappedQuery = FALSE), tag = tags)) This error goes away if we don't include "XS" in tags, also if we use version 1.0.0 of Rsamtools. Any ideas? The sessionInfo() output is below. Thanks in advance! --Misha > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-unknown-linux-gnu locale: [1] C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rsamtools_1.1.11 Biostrings_2.16.9 GenomicRanges_1.0.7 [4] IRanges_1.6.11 svMisc_0.9-57 JavaGD_0.5-2 [7] rJava_0.8-4 loaded via a namespace (and not attached): [1] Biobase_2.8.0 On Thu, 12 Aug 2010, Andrew Tikhonov wrote: > Dear Biocore Team, > > We've got a problem where 'Rsamtools' produces segfaults and > core-dumps when reading a .bam file using the "XS" tag. We have a faulty .bam > and the list or R commands to reproduce it. Could you please point us to > someone who we may discuss this matter with and, if possible, fix the > problem. > > Thanks a lot in advance. > > Regards, > Andrew > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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