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Question: gmapR/gsnap crashes
0
gravatar for Tim Triche
6.0 years ago by
Tim Triche4.2k
United States
Tim Triche4.2k wrote:
I was interested in comparing gsnap to subread, so I followed the instructions provided in the gmapR vignette (BioC-2.11, stable version) and created an hg18 genome, etc. to realign some ChIP-seq data. Unfortunately, the aligner did not seem to like any of the reads I fed it (I tried several, including SRA archives SRR094809 and SRR350216). Do the following error messages set off red flags for anyone? Looking for index files in directory /home/ttriche/FASTQ/gmapR/Hsapiens/hg18 Gammaptrs file is hg18.ref12153gammaptrs Offsetscomp file is hg18.ref12153offsetscomp Positions file is hg18.ref12153positions Allocating memory for ref gammaptrs, kmer 15, interval 3...done (67,108,868 bytes, 0.78 sec) Allocating memory for ref offsets, kmer 15, interval 3...done (349,702,436 bytes, 3.86 sec) Pre-loading ref positions, kmer 15, interval 3... done (2,990,309,376 bytes, 730056 pages, 32.16 sec). GMAP modes: pairsearch, terminal, improvement Starting alignment Signal received: Segmentation fault Problem sequence: CD133.H3K79me2.41 (36 bp) >CD133.H3K79me2.41 NCCAACATGTTAAAACCCTTTCTCTACTAAAAACAC sh: line 1: 13517 Aborted /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap --db=hg18 --dir=/home/ttriche/FASTQ/gmapR/Hsapiens --nthreads=12 --npaths=10 --quiet-if-excessive --nofails --format=sam CD133.H3K79me2.fastq > CD133.H3K79me2.sam GSNAP version 2011-12-28 called with args: /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap --db= --version A GsnapOutput Object path: CD133.H3K79me2.sam I'm running the stable version: R> packageVersion('gmapR') [1] ‘1.0.0’ And here is the rest... R> sessionInfo() R version 2.15.2 (2012-10-26) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GmapGenome.Hsapiens.UCSC.hg18_1.0.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [3] BSgenome_1.26.1 Biostrings_2.26.2 [5] gmapR_1.0.0 GenomicRanges_1.10.6 [7] IRanges_1.16.4 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 [4] bitops_1.0-5 DBI_0.2-5 GenomicFeatures_1.10.1 [7] parallel_2.15.2 RCurl_1.95-3 Rsamtools_1.10.2 [10] RSQLite_0.11.2 rtracklayer_1.18.2 stats4_2.15.2 [13] tools_2.15.2 VariantAnnotation_1.4.8 XML_3.95-0.1 [16] zlibbioc_1.4.0 Thanks for any assistance, --t -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
gmapr • 1.2k views
ADD COMMENTlink modified 6.0 years ago by Michael Lawrence10k • written 6.0 years ago by Tim Triche4.2k
Answer: gmapR/gsnap crashes
0
gravatar for Michael Lawrence
6.0 years ago by
United States
Michael Lawrence10k wrote:
I've asked Tom Wu and he pointed out that your genome index may be truncated, since there should be more than 2,990,309,376 bytes for an hg18 index. More like 3,841,790,404 bytes. Perhaps you could try rebuilding the genome index? Thanks, Michael On Tue, Feb 5, 2013 at 11:43 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > I was interested in comparing gsnap to subread, so I followed the > instructions provided in the gmapR vignette (BioC-2.11, stable version) and > created an hg18 genome, etc. to realign some ChIP-seq data. > > Unfortunately, the aligner did not seem to like any of the reads I fed it > (I tried several, including SRA archives SRR094809 and SRR350216). Do the > following error messages set off red flags for anyone? > > Looking for index files in directory > /home/ttriche/FASTQ/gmapR/Hsapiens/hg18 > Gammaptrs file is hg18.ref12153gammaptrs > Offsetscomp file is hg18.ref12153offsetscomp > Positions file is hg18.ref12153positions > Allocating memory for ref gammaptrs, kmer 15, interval 3...done (67,108,868 > bytes, 0.78 sec) > Allocating memory for ref offsets, kmer 15, interval 3...done (349,702,436 > bytes, 3.86 sec) > Pre-loading ref positions, kmer 15, interval 3... done (2,990,309,376 > bytes, 730056 pages, 32.16 sec). > GMAP modes: pairsearch, terminal, improvement > Starting alignment > Signal received: Segmentation fault > Problem sequence: CD133.H3K79me2.41 (36 bp) > >CD133.H3K79me2.41 > NCCAACATGTTAAAACCCTTTCTCTACTAAAAACAC > sh: line 1: 13517 Aborted > /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap > --db=hg18 --dir=/home/ttriche/FASTQ/gmapR/Hsapiens --nthreads=12 > --npaths=10 --quiet-if-excessive --nofails --format=sam > CD133.H3K79me2.fastq > CD133.H3K79me2.sam > GSNAP version 2011-12-28 called with args: > /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap > --db= --version > A GsnapOutput Object > path: CD133.H3K79me2.sam > > I'm running the stable version: > > R> packageVersion('gmapR') > [1] ‘1.0.0’ > > And here is the rest... > > R> sessionInfo() > R version 2.15.2 (2012-10-26) > 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=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GmapGenome.Hsapiens.UCSC.hg18_1.0.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19 > [3] BSgenome_1.26.1 Biostrings_2.26.2 > [5] gmapR_1.0.0 GenomicRanges_1.10.6 > [7] IRanges_1.16.4 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 > [4] bitops_1.0-5 DBI_0.2-5 GenomicFeatures_1.10.1 > [7] parallel_2.15.2 RCurl_1.95-3 Rsamtools_1.10.2 > [10] RSQLite_0.11.2 rtracklayer_1.18.2 stats4_2.15.2 > [13] tools_2.15.2 VariantAnnotation_1.4.8 XML_3.95-0.1 > [16] zlibbioc_1.4.0 > > > Thanks for any assistance, > > --t > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by Michael Lawrence10k
Will do, thanks! --t On Feb 7, 2013, at 12:32 PM, Michael Lawrence <lawrence.michael@gene.com> wrote: > I've asked Tom Wu and he pointed out that your genome index may be truncated, since there should be more than 2,990,309,376 bytes for an hg18 index. More like 3,841,790,404 bytes. Perhaps you could try rebuilding the genome index? > > Thanks, > Michael > > > > > On Tue, Feb 5, 2013 at 11:43 AM, Tim Triche, Jr. <tim.triche@gmail.com> wrote: >> I was interested in comparing gsnap to subread, so I followed the >> instructions provided in the gmapR vignette (BioC-2.11, stable version) and >> created an hg18 genome, etc. to realign some ChIP-seq data. >> >> Unfortunately, the aligner did not seem to like any of the reads I fed it >> (I tried several, including SRA archives SRR094809 and SRR350216). Do the >> following error messages set off red flags for anyone? >> >> Looking for index files in directory /home/ttriche/FASTQ/gmapR/Hsapiens/hg18 >> Gammaptrs file is hg18.ref12153gammaptrs >> Offsetscomp file is hg18.ref12153offsetscomp >> Positions file is hg18.ref12153positions >> Allocating memory for ref gammaptrs, kmer 15, interval 3...done (67,108,868 >> bytes, 0.78 sec) >> Allocating memory for ref offsets, kmer 15, interval 3...done (349,702,436 >> bytes, 3.86 sec) >> Pre-loading ref positions, kmer 15, interval 3... done (2,990,309,376 >> bytes, 730056 pages, 32.16 sec). >> GMAP modes: pairsearch, terminal, improvement >> Starting alignment >> Signal received: Segmentation fault >> Problem sequence: CD133.H3K79me2.41 (36 bp) >> >CD133.H3K79me2.41 >> NCCAACATGTTAAAACCCTTTCTCTACTAAAAACAC >> sh: line 1: 13517 Aborted >> /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap >> --db=hg18 --dir=/home/ttriche/FASTQ/gmapR/Hsapiens --nthreads=12 >> --npaths=10 --quiet-if-excessive --nofails --format=sam >> CD133.H3K79me2.fastq > CD133.H3K79me2.sam >> GSNAP version 2011-12-28 called with args: >> /home/ttriche/R/x86_64-unknown-linux-gnu- library/2.15/gmapR/usr/bin/gsnap >> --db= --version >> A GsnapOutput Object >> path: CD133.H3K79me2.sam >> >> I'm running the stable version: >> >> R> packageVersion('gmapR') >> [1] ‘1.0.0’ >> >> And here is the rest... >> >> R> sessionInfo() >> R version 2.15.2 (2012-10-26) >> 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=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] GmapGenome.Hsapiens.UCSC.hg18_1.0.0 BSgenome.Hsapiens.UCSC.hg18_1.3.19 >> [3] BSgenome_1.26.1 Biostrings_2.26.2 >> [5] gmapR_1.0.0 GenomicRanges_1.10.6 >> [7] IRanges_1.16.4 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.20.3 Biobase_2.18.0 biomaRt_2.14.0 >> [4] bitops_1.0-5 DBI_0.2-5 GenomicFeatures_1.10.1 >> [7] parallel_2.15.2 RCurl_1.95-3 Rsamtools_1.10.2 >> [10] RSQLite_0.11.2 rtracklayer_1.18.2 stats4_2.15.2 >> [13] tools_2.15.2 VariantAnnotation_1.4.8 XML_3.95-0.1 >> [16] zlibbioc_1.4.0 >> >> >> Thanks for any assistance, >> >> --t >> >> -- >> *A model is a lie that helps you see the truth.* >> * >> * >> Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Tim Triche4.2k
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