Question

error reading bismark sam/bam files

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kamal.fartiyal84 ▴ 10

@kamalfartiyal84-7976

Last seen 5.9 years ago

Cancer Research UK Cambridge Institute

I am getting the following error on reading bismark sorted sam/bam files. Its crashing the R session everytime. The sam/bam files are sorted by samtools.

> my.methRaw=processBismarkAln( location = paths[i], sample.id=samples[i], treatment=grps[i],assembly="hg19", read.context="CpG", save.folder=savefolder)

*** caught segfault ***

address 0x2b0, cause 'memory not mapped'

Traceback:

1: .Call("methylKit_methCall", PACKAGE = "methylKit", read1, type, nolap, minqual, mincov, phred64, CpGfile, CHHfile, CHGfile)

2: methCall(read1 = location, type = "bam", nolap = nolap, minqual = minqual, mincov = mincov, phred64 = phred64, CpGfile = out.files[["CpG"]], CHHfile = out.files[["CHH"]], CHGfile = out.files[["CHG"]])

3: .local(location, sample.id, assembly, save.folder, save.context, read.context, nolap, mincov, minqual, phred64, save.db)

4: processBismarkAln(location[[i]], sample.id[[i]], assembly, save.folder, save.context, read.context, nolap, mincov, minqual, phred64)

5: processBismarkAln(location[[i]], sample.id[[i]], assembly, save.folder, save.context, read.context, nolap, mincov, minqual, phred64)

6: processBismarkAln(location = paths[i], sample.id = samples[i], treatment = grps[i], assembly = "hg19", read.context = "CpG", save.folder = savefolder)

7: processBismarkAln(location = paths[i], sample.id = samples[i], treatment = grps[i], assembly = "hg19", read.context = "CpG", save.folder = savefolder)

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 3.3.1 (2016-06-21)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

locale:

[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C

[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8

[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8

[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C

[9] LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] parallel stats4 stats graphics grDevices utils datasets

[8] methods base

other attached packages:

[1] methylKit_1.0.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3

[4] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0

methylKit • 2.0k views

ADD COMMENT • link 7.5 years ago kamal.fartiyal84 ▴ 10

score 0 · Answer 1 · 2017-06-16

Try to update your R and BioC, and retry. Also have a look at the similar problems mentioned here: https://groups.google.com/forum/#!forum/methylkit_discussion On Fri, Jun 16, 2017 at 1:34 PM, kamal.fartiyal84 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User kamal.fartiyal84 <https: support.bioconductor.org="" u="" 7976=""/> wrote Question: > error reading bismark sam/bam files > <https: support.bioconductor.org="" p="" 97138=""/>: > > I am getting the following error on reading bismark sorted sam/bam files. > Its crashing the R session everytime. The sam/bam files are sorted by > samtools. > > > > > my.methRaw=processBismarkAln( location = paths[i], sample.id=samples[i], > treatment=grps[i],assembly="hg19", read.context="CpG", > save.folder=savefolder) > > > > *** caught segfault *** > > address 0x2b0, cause 'memory not mapped' > > > > Traceback: > > 1: .Call("methylKit_methCall", PACKAGE = "methylKit", read1, type, > nolap, minqual, mincov, phred64, CpGfile, CHHfile, CHGfile) > > 2: methCall(read1 = location, type = "bam", nolap = nolap, minqual = > minqual, mincov = mincov, phred64 = phred64, CpGfile = > out.files[["CpG"]], CHHfile = out.files[["CHH"]], CHGfile = > out.files[["CHG"]]) > > 3: .local(location, sample.id, assembly, save.folder, save.context, > read.context, nolap, mincov, minqual, phred64, save.db) > > 4: processBismarkAln(location[[i]], sample.id[[i]], assembly, > save.folder, save.context, read.context, nolap, mincov, minqual, > phred64) > > 5: processBismarkAln(location[[i]], sample.id[[i]], assembly, > save.folder, save.context, read.context, nolap, mincov, minqual, > phred64) > > 6: processBismarkAln(location = paths[i], sample.id = samples[i], > treatment = grps[i], assembly = "hg19", read.context = "CpG", > save.folder = savefolder) > > 7: processBismarkAln(location = paths[i], sample.id = samples[i], > treatment = grps[i], assembly = "hg19", read.context = "CpG", > save.folder = savefolder) > > > > 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 3.3.1 (2016-06-21) > > Platform: x86_64-pc-linux-gnu (64-bit) > > Running under: CentOS Linux 7 (Core) > > > > locale: > > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats4 stats graphics grDevices utils datasets > > [8] methods base > > > > other attached packages: > > [1] methylKit_1.0.0 GenomicRanges_1.26.4 GenomeInfoDb_1.10.3 > > [4] IRanges_2.8.2 S4Vectors_0.12.2 BiocGenerics_0.20.0 > > ------------------------------ > > Post tags: methylKit > > You may reply via email or visit error reading bismark sam/bam files >

score 0 · Answer 2 · 2017-06-16

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