Genominator error when calling syste.time
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Boel Brynedal ▴ 200
@boel-brynedal-2091
Last seen 10.3 years ago
Hi All, I am analyzing some ChIP seq data using DESeq, reads have all been aligned and are in BAM format. "aligned" in a names character vector containing the names of the bam files. I'm trying to use the Genominator function importFromAlignedReads to read in the aligned data, but I get an error regarding the system.time function: > aligned 20417.6.bam 2041T.6.bam 305AG.8.bam 305D0.8.bam "20417.6.bam" "2041T.6.bam" "305AG.8.bam" "305D0.8.bam" > chroms [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [10] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [19] "chr19" "chr20" "chr21" "chrX" "chrY" "chrM" > eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) Error in system.time(exp) : Unable to write the table, delete table or specify overwrite. In addition: Warning message: In value[[3L]](cond) : RS-DBI driver: (error in statement: near "20417.6": syntax error) Timing stopped at: 0.076 0 0.081 Timing stopped at: 12.851 0.74 13.631 Any idea what might be wrong, anyone seem a similar issue earlier? Seems to be the second call to system.time within importFromAlignedReads that breaks the function. > sessionInfo() R version 2.15.0 (2012-03-30) 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] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Genominator_1.10.0 GenomeGraphs_1.16.0 biomaRt_2.12.0 [4] RSQLite_0.11.1 DBI_0.2-5 ShortRead_1.14.1 [7] latticeExtra_0.6-19 RColorBrewer_1.0-5 Rsamtools_1.8.0 [10] lattice_0.20-6 Biostrings_2.24.1 GenomicRanges_1.8.3 [13] IRanges_1.14.2 DESeq_1.8.1 locfit_1.5-7 [16] Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.3 loaded via a namespace (and not attached): [1] annotate_1.34.0 AnnotationDbi_1.18.0 bitops_1.0-4.1 [4] genefilter_1.38.0 geneplotter_1.34.0 hwriter_1.3 [7] RCurl_1.91-1 splines_2.15.0 stats4_2.15.0 [10] survival_2.36-12 tools_2.15.0 XML_3.9-4 [13] xtable_1.7-0 zlibbioc_1.2.0 [[alternative HTML version deleted]]
Genominator DESeq Genominator DESeq • 1.5k views
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@kasper-daniel-hansen-2979
Last seen 18 months ago
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On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) > Error in system.time(exp) : > ?Unable to write the table, delete table or specify overwrite. > In addition: Warning message: > In value[[3L]](cond) : > ?RS-DBI driver: (error in statement: near "20417.6": syntax error) > Timing stopped at: 0.076 0 0.081 > Timing stopped at: 12.851 0.74 13.631 The system.time is a red herring I think. Note that it says > ?Unable to write the table, delete table or specify overwrite. I suggest you have too little disk space, or permission issues. Kasper
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[CC'ing Genominator maintainer] On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) >> Error in system.time(exp) : >> ?Unable to write the table, delete table or specify overwrite. >> In addition: Warning message: >> In value[[3L]](cond) : >> ?RS-DBI driver: (error in statement: near "20417.6": syntax error) >> Timing stopped at: 0.076 0 0.081 >> Timing stopped at: 12.851 0.74 13.631 > > The system.time is a red herring I think. ?Note that it says > ?> ?Unable to write the table, delete table or specify overwrite. > I suggest you have too little disk space, or permission issues. > It seems that the warning is significant as well. Looks like the package is trying to use the names of your BAM files in a SQL query but that query is malformed. Dan > Kasper > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Sounds reasonable, probably because the column names will start with numbers. Kasper On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > [CC'ing Genominator maintainer] > > On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen > <kasperdanielhansen at="" gmail.com=""> wrote: >> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) >>> Error in system.time(exp) : >>> ?Unable to write the table, delete table or specify overwrite. >>> In addition: Warning message: >>> In value[[3L]](cond) : >>> ?RS-DBI driver: (error in statement: near "20417.6": syntax error) >>> Timing stopped at: 0.076 0 0.081 >>> Timing stopped at: 12.851 0.74 13.631 >> >> The system.time is a red herring I think. ?Note that it says >> ?> ?Unable to write the table, delete table or specify overwrite. >> I suggest you have too little disk space, or permission issues. >> > > It seems that the warning is significant as well. Looks like the > package is trying to use the names of your BAM files in a SQL query > but that query is malformed. > > Dan > > >> Kasper >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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I have 12 GB of RAM for this job, and the BAM files are not particularly big. Is it likely that this is a memory issue? I'm writing the files in my own folder on a larger cluster, so there should not be a problem with permissions. Or? How can I investigate whether this is a permission issue? Changing the names of aligned did get rid of the warning however. > eData <- importFromAlignedReads(aligned, dbFilename='/fg/cogdec/Boel /Marga/test/test.db',tablename='raw',type="BAM") Error in match(chromosome(aln), chrMap) : error in evaluating the argument 'table' in selecting a method for function 'match': Error: argument "chrMap" is missing, with no default Timing stopped at: 6.628 0.001 6.63 On my MacBook pro I am able to get this function to work (same packages, using R.12.) Using R.12.1 on the cluster I get: > eData <- importFromAlignedReads(aligned, chrMap=chroms,dbFilename='test.db',tablename='raw',type="BAM") Error in system.time(exp) : Unable to write the table, delete table or specify overwrite. In addition: Warning message: In value[[3L]](cond) : RS-DBI driver: (error in statement: near ".6": syntax error) Timing stopped at: 0.053 0.001 0.056 Timing stopped at: 12.552 0.633 13.228 Any suggestions highly appreciated! Boel ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com] Sent: Wednesday, April 11, 2012 3:57 PM To: Dan Tenenbaum Cc: Boel Brynedal; bioconductor at r-project.org; James Bullard Subject: Re: [BioC] Genominator error when calling syste.time Sounds reasonable, probably because the column names will start with numbers. Kasper On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > [CC'ing Genominator maintainer] > > On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen > <kasperdanielhansen at="" gmail.com=""> wrote: >> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) >>> Error in system.time(exp) : >>> Unable to write the table, delete table or specify overwrite. >>> In addition: Warning message: >>> In value[[3L]](cond) : >>> RS-DBI driver: (error in statement: near "20417.6": syntax error) >>> Timing stopped at: 0.076 0 0.081 >>> Timing stopped at: 12.851 0.74 13.631 >> >> The system.time is a red herring I think. Note that it says >> > Unable to write the table, delete table or specify overwrite. >> I suggest you have too little disk space, or permission issues. >> > > It seems that the warning is significant as well. Looks like the > package is trying to use the names of your BAM files in a SQL query > but that query is malformed. > > Dan > > >> Kasper >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Thu, Apr 12, 2012 at 11:15 AM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: > I have 12 GB of RAM for this job, and the BAM files are not particularly big. Is it likely that this is a memory issue? I'm writing the files in my own folder on a larger cluster, so there should not be a problem with permissions. Or? How can I investigate whether this is a permission issue? > > Changing the names of aligned did get rid of the warning however. > >> eData <- importFromAlignedReads(aligned, dbFilename='/fg/cogdec/Boe l/Marga/test/test.db',tablename='raw',type="BAM") > Error in match(chromosome(aln), chrMap) : > ?error in evaluating the argument 'table' in selecting a method for function 'match': Error: argument "chrMap" is missing, with no default > Timing stopped at: 6.628 0.001 6.63 You are missing the chrMap=chroms you use below. > On my MacBook pro I am able to get this function to work (same packages, using R.12.) > > Using R.12.1 on the cluster I get: > >> eData <- importFromAlignedReads(aligned, chrMap=chroms,dbFilename='test.db',tablename='raw',type="BAM") > Error in system.time(exp) : > ?Unable to write the table, delete table or specify overwrite. > In addition: Warning message: > In value[[3L]](cond) : > ?RS-DBI driver: (error in statement: near ".6": syntax error) > Timing stopped at: 0.053 0.001 0.056 > Timing stopped at: 12.552 0.633 13.228 > The names of the columns in the table has to by valid names according to the SQL syntax. This precludes the use of *.*. Instead of renaming the files you could so something like names(aligned) = c("sample1", "sample2", ...) then the column names will be the names of the aligned vector. Kasper > Any suggestions highly appreciated! > Boel > > > ________________________________________ > From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com] > Sent: Wednesday, April 11, 2012 3:57 PM > To: Dan Tenenbaum > Cc: Boel Brynedal; bioconductor at r-project.org; James Bullard > Subject: Re: [BioC] Genominator error when calling syste.time > > Sounds reasonable, probably because the column names will start with numbers. > > Kasper > > On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> [CC'ing Genominator maintainer] >> >> On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen >> <kasperdanielhansen at="" gmail.com=""> wrote: >>> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >>>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) >>>> Error in system.time(exp) : >>>> ?Unable to write the table, delete table or specify overwrite. >>>> In addition: Warning message: >>>> In value[[3L]](cond) : >>>> ?RS-DBI driver: (error in statement: near "20417.6": syntax error) >>>> Timing stopped at: 0.076 0 0.081 >>>> Timing stopped at: 12.851 0.74 13.631 >>> >>> The system.time is a red herring I think. ?Note that it says >>> ?> ?Unable to write the table, delete table or specify overwrite. >>> I suggest you have too little disk space, or permission issues. >>> >> >> It seems that the warning is significant as well. Looks like the >> package is trying to use the names of your BAM files in a SQL query >> but that query is malformed. >> >> Dan >> >> >>> Kasper >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Changing to very vanilla names in the sample vector and actually giving the chroms vector (...) solved the problem. Thanks! ________________________________________ From: Kasper Daniel Hansen [kasperdanielhansen@gmail.com] Sent: Thursday, April 12, 2012 11:45 AM To: Boel Brynedal Cc: Dan Tenenbaum; bioconductor at r-project.org; James Bullard Subject: Re: [BioC] Genominator error when calling syste.time On Thu, Apr 12, 2012 at 11:15 AM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: > I have 12 GB of RAM for this job, and the BAM files are not particularly big. Is it likely that this is a memory issue? I'm writing the files in my own folder on a larger cluster, so there should not be a problem with permissions. Or? How can I investigate whether this is a permission issue? > > Changing the names of aligned did get rid of the warning however. > >> eData <- importFromAlignedReads(aligned, dbFilename='/fg/cogdec/Boe l/Marga/test/test.db',tablename='raw',type="BAM") > Error in match(chromosome(aln), chrMap) : > error in evaluating the argument 'table' in selecting a method for function 'match': Error: argument "chrMap" is missing, with no default > Timing stopped at: 6.628 0.001 6.63 You are missing the chrMap=chroms you use below. > On my MacBook pro I am able to get this function to work (same packages, using R.12.) > > Using R.12.1 on the cluster I get: > >> eData <- importFromAlignedReads(aligned, chrMap=chroms,dbFilename='test.db',tablename='raw',type="BAM") > Error in system.time(exp) : > Unable to write the table, delete table or specify overwrite. > In addition: Warning message: > In value[[3L]](cond) : > RS-DBI driver: (error in statement: near ".6": syntax error) > Timing stopped at: 0.053 0.001 0.056 > Timing stopped at: 12.552 0.633 13.228 > The names of the columns in the table has to by valid names according to the SQL syntax. This precludes the use of *.*. Instead of renaming the files you could so something like names(aligned) = c("sample1", "sample2", ...) then the column names will be the names of the aligned vector. Kasper > Any suggestions highly appreciated! > Boel > > > ________________________________________ > From: Kasper Daniel Hansen [kasperdanielhansen at gmail.com] > Sent: Wednesday, April 11, 2012 3:57 PM > To: Dan Tenenbaum > Cc: Boel Brynedal; bioconductor at r-project.org; James Bullard > Subject: Re: [BioC] Genominator error when calling syste.time > > Sounds reasonable, probably because the column names will start with numbers. > > Kasper > > On Wed, Apr 11, 2012 at 3:46 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> [CC'ing Genominator maintainer] >> >> On Wed, Apr 11, 2012 at 12:41 PM, Kasper Daniel Hansen >> <kasperdanielhansen at="" gmail.com=""> wrote: >>> On Wed, Apr 11, 2012 at 3:32 PM, Boel Brynedal <boel.brynedal at="" ki.se=""> wrote: >>>>> eData <- importFromAlignedReads(aligned, chrMap=chroms, dbFilename='test.db', tablename='raw', type="BAM", verbose=FALSE) >>>> Error in system.time(exp) : >>>> Unable to write the table, delete table or specify overwrite. >>>> In addition: Warning message: >>>> In value[[3L]](cond) : >>>> RS-DBI driver: (error in statement: near "20417.6": syntax error) >>>> Timing stopped at: 0.076 0 0.081 >>>> Timing stopped at: 12.851 0.74 13.631 >>> >>> The system.time is a red herring I think. Note that it says >>> > Unable to write the table, delete table or specify overwrite. >>> I suggest you have too little disk space, or permission issues. >>> >> >> It seems that the warning is significant as well. Looks like the >> package is trying to use the names of your BAM files in a SQL query >> but that query is malformed. >> >> Dan >> >> >>> Kasper >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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