ParseMetaFromGtfFile is.na() error

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Hi, I am using SCAN.UPC and trying to create an annotation file from one concatenated GRCm38.73 fasta file. I have the matched GRCm38.73.gtf file. The .gtf file parsing halts near the end of the file and the following error message appears and no output file is generated. Thanks, Beth ... Done parsing 1140000 lines from /Mus_musculus.GRCm38. 73.gtf Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) 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 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SCAN.UPC_2.6.0 sva_3.10.0 mgcv_1.7-29 [4] nlme_3.1-117 corpcor_1.6.6 foreach_1.4.2 [7] affyio_1.32.0 affy_1.42.2 GEOquery_2.30.0 [10] oligo_1.28.2 Biostrings_2.32.0 XVector_0.4.0 [13] IRanges_1.22.2 oligoClasses_1.26.0 Biobase_2.24.0 [16] BiocGenerics_0.10.0 limma_3.20.1 Rsubread_1.14.0 [19] BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affxparser_1.36.0 bit_1.1-12 codetools_0.2-8 [4] DBI_0.2-7 ff_2.2-13 GenomeInfoDb_1.0.1 [7] GenomicRanges_1.16.0 grid_3.1.0 iterators_1.0.7 [10] lattice_0.20-29 MASS_7.3-31 Matrix_1.1-3 [13] preprocessCore_1.26.1 RCurl_1.95-4.1 splines_3.1.0 [16] stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 [19] zlibbioc_1.10.0 > -- Sent via the guest posting facility at bioconductor.org.

Annotation SCAN.UPC Annotation SCAN.UPC • 1.4k views

ADD COMMENT • link updated 10.5 years ago by Michael Lawrence ★ 11k • written 10.5 years ago by Guest User ★ 13k

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Michael Lawrence ★ 11k

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What was the actual code that produced the error? It looks like this is from GenomicFeatures? On Thu, Jun 5, 2014 at 10:38 AM, Beth Wilmot [guest] <guest@bioconductor.org> wrote: > Hi, > I am using SCAN.UPC and trying to create an annotation file from one > concatenated GRCm38.73 fasta file. I have the matched GRCm38.73.gtf file. > The .gtf file parsing halts near the end of the file and the following > error message appears and no output file is generated. Thanks, Beth > > ... > Done parsing 1140000 lines from /Mus_musculus.GRCm38. > 73.gtf > Warning message: > In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > -- output of sessionInfo(): > > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > 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 stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] SCAN.UPC_2.6.0 sva_3.10.0 mgcv_1.7-29 > [4] nlme_3.1-117 corpcor_1.6.6 foreach_1.4.2 > [7] affyio_1.32.0 affy_1.42.2 GEOquery_2.30.0 > [10] oligo_1.28.2 Biostrings_2.32.0 XVector_0.4.0 > [13] IRanges_1.22.2 oligoClasses_1.26.0 Biobase_2.24.0 > [16] BiocGenerics_0.10.0 limma_3.20.1 Rsubread_1.14.0 > [19] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.36.0 bit_1.1-12 codetools_0.2-8 > [4] DBI_0.2-7 ff_2.2-13 GenomeInfoDb_1.0.1 > [7] GenomicRanges_1.16.0 grid_3.1.0 iterators_1.0.7 > [10] lattice_0.20-29 MASS_7.3-31 Matrix_1.1-3 > [13] preprocessCore_1.26.1 RCurl_1.95-4.1 splines_3.1.0 > [16] stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 > [19] zlibbioc_1.10.0 > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 COMMENT • link 10.5 years ago Michael Lawrence ★ 11k

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My code is: ParseMetaFromGtfFile("mm10/Mus_musculus.GRCm38.73.gtf",fastaFilePatter n="mm10/Mus_musculus.GRCm38.73.fa",outFilePath="mm10/GRCh38_Annotation .txt",featureTypes=c("protein_coding"),attributeType="gene_id") Thanks, Beth From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Thursday, June 05, 2014 11:23 AM To: Beth Wilmot [guest] Cc: bioconductor@r-project.org; Beth Wilmot; SCAN.UPC Maintainer Subject: Re: [BioC] ParseMetaFromGtfFile is.na() error What was the actual code that produced the error? It looks like this is from GenomicFeatures? On Thu, Jun 5, 2014 at 10:38 AM, Beth Wilmot [guest] <guest@bioconductor.org<mailto:guest@bioconductor.org>> wrote: Hi, I am using SCAN.UPC and trying to create an annotation file from one concatenated GRCm38.73 fasta file. I have the matched GRCm38.73.gtf file. The .gtf file parsing halts near the end of the file and the following error message appears and no output file is generated. Thanks, Beth ... Done parsing 1140000 lines from /Mus_musculus.GRCm38. 73.gtf Warning message: In is.na<http: is.na="">(x) : is.na<http: is.na="">() applied to non-(list or vector) of type 'NULL' -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) 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 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] SCAN.UPC_2.6.0 sva_3.10.0 mgcv_1.7-29 [4] nlme_3.1-117 corpcor_1.6.6 foreach_1.4.2 [7] affyio_1.32.0 affy_1.42.2 GEOquery_2.30.0 [10] oligo_1.28.2 Biostrings_2.32.0 XVector_0.4.0 [13] IRanges_1.22.2 oligoClasses_1.26.0 Biobase_2.24.0 [16] BiocGenerics_0.10.0 limma_3.20.1 Rsubread_1.14.0 [19] BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affxparser_1.36.0 bit_1.1-12 codetools_0.2-8 [4] DBI_0.2-7 ff_2.2-13 GenomeInfoDb_1.0.1 [7] GenomicRanges_1.16.0 grid_3.1.0 iterators_1.0.7 [10] lattice_0.20-29 MASS_7.3-31 Matrix_1.1-3 [13] preprocessCore_1.26.1 RCurl_1.95-4.1 splines_3.1.0 [16] stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 [19] zlibbioc_1.10.0 > -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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 REPLY • link 10.5 years ago Beth Wilmot ▴ 120

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Looks like SCAN.UPC has implemented yet another GTF parser.... On Thu, Jun 5, 2014 at 11:27 AM, Beth Wilmot <wilmotb@ohsu.edu> wrote: > My code is: > > > ParseMetaFromGtfFile("mm10/Mus_musculus.GRCm38.73.gtf",fastaFilePatt ern="mm10/Mus_musculus.GRCm38.73.fa",outFilePath="mm10/GRCh38_Annotati on.txt",featureTypes=c("protein_coding"),attributeType="gene_id") > > > > Thanks, > Beth > > > > *From:* Michael Lawrence [mailto:lawrence.michael@gene.com] > *Sent:* Thursday, June 05, 2014 11:23 AM > *To:* Beth Wilmot [guest] > *Cc:* bioconductor@r-project.org; Beth Wilmot; SCAN.UPC Maintainer > *Subject:* Re: [BioC] ParseMetaFromGtfFile is.na() error > > > > What was the actual code that produced the error? It looks like this is > from GenomicFeatures? > > > > On Thu, Jun 5, 2014 at 10:38 AM, Beth Wilmot [guest] < > guest@bioconductor.org> wrote: > > Hi, > I am using SCAN.UPC and trying to create an annotation file from one > concatenated GRCm38.73 fasta file. I have the matched GRCm38.73.gtf file. > The .gtf file parsing halts near the end of the file and the following > error message appears and no output file is generated. Thanks, Beth > > ... > Done parsing 1140000 lines from /Mus_musculus.GRCm38. > 73.gtf > Warning message: > In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > -- output of sessionInfo(): > > > > > sessionInfo() > R version 3.1.0 (2014-04-10) > 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 stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] SCAN.UPC_2.6.0 sva_3.10.0 mgcv_1.7-29 > [4] nlme_3.1-117 corpcor_1.6.6 foreach_1.4.2 > [7] affyio_1.32.0 affy_1.42.2 GEOquery_2.30.0 > [10] oligo_1.28.2 Biostrings_2.32.0 XVector_0.4.0 > [13] IRanges_1.22.2 oligoClasses_1.26.0 Biobase_2.24.0 > [16] BiocGenerics_0.10.0 limma_3.20.1 Rsubread_1.14.0 > [19] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.36.0 bit_1.1-12 codetools_0.2-8 > [4] DBI_0.2-7 ff_2.2-13 GenomeInfoDb_1.0.1 > [7] GenomicRanges_1.16.0 grid_3.1.0 iterators_1.0.7 > [10] lattice_0.20-29 MASS_7.3-31 Matrix_1.1-3 > [13] preprocessCore_1.26.1 RCurl_1.95-4.1 splines_3.1.0 > [16] stats4_3.1.0 tools_3.1.0 XML_3.98-1.1 > [19] zlibbioc_1.10.0 > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 REPLY • link 10.5 years ago Michael Lawrence ★ 11k

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