Question

Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"

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samupatt • 0

@samupatt-16298

Last seen 6.4 years ago

Commands entered:

> library('customProDB')
> library('rtracklayer')
> session <- browserSession()
> genome(session) <- 'hg19'
> dbsnps <- trackNames(session)[grep('snp', trackNames(session), fixed=T)]

> PrepareAnnotationRefseq(genome='hg19', CDSfasta="/home/shp12/UCSCData/refsequcsc.fasta", pepfasta="/home/shp12/UCSCData/refpepucsc.fasta", annotation_path="/home/shp12/Annotation_data")

Error obtained:

PrepareAnnotationRefseq(genome='hg19', CDSfasta="/home/shp12/UCSCData/refsequcsc.fasta", pepfasta="/home/shp12/UCSCData/refpeBuild TranscriptDB object (txdb.sqlite) ... nnotation_data")

Error in .tablename2track(tablename, session) :
UCSC table "refGene" is not supported

sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.so

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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] customProDB_1.18.0   BiocInstaller_1.28.0 rtracklayer_1.38.3
[4] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 biomaRt_2.34.2
[7] AnnotationDbi_1.40.0 Biobase_2.38.0       IRanges_2.12.0
[10] S4Vectors_0.16.0     BiocGenerics_0.24.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.17               plyr_1.8.4
[3] compiler_3.4.1             XVector_0.18.0
[5] GenomicFeatures_1.30.3     prettyunits_1.0.2
[7] bitops_1.0-6               tools_3.4.1
[9] progress_1.2.0             zlibbioc_1.24.0
[11] digest_0.6.15              bit_1.1-14
[13] AhoCorasickTrie_0.1.0      BSgenome_1.46.0
[15] lattice_0.20-35            RSQLite_2.1.1
[17] memoise_1.1.0              pkgconfig_2.0.1
[19] rlang_0.2.1                Matrix_1.2-10
[21] DelayedArray_0.4.1         DBI_1.0.0
[23] GenomeInfoDbData_1.0.0     stringr_1.3.1
[25] httr_1.3.1                 Biostrings_2.46.0
[27] hms_0.4.2                  grid_3.4.1
[29] bit64_0.9-7                R6_2.2.2
[31] RMySQL_0.10.15             XML_3.98-1.11
[33] BiocParallel_1.12.0        blob_1.1.1
[35] magrittr_1.5               matrixStats_0.53.1
[37] GenomicAlignments_1.14.2   Rsamtools_1.30.0
[39] SummarizedExperiment_1.8.1 assertthat_0.2.0
[41] stringi_1.2.3              RCurl_1.95-4.10
[43] VariantAnnotation_1.24.5   crayon_1.3.4
>

Head of Sequence and Peptide files in question:

Pep:>NP_001337147.1
MMEGLKKRTRKAFGIRKKEKDTDSTGSPDRDGIKKSNGAPNGFYAEIDWE
RYNSPELDEEGYSIRPEEPGSTKGKHFYSSSESEEEEESHKKFNIKIKPL
QSKDILKNAATVDELKASIGNIALSPSPVRKSPRRSPGAIKRNLSSEEVA

Seq:
>hg19_refGene_NM_001350218 range=chr1:67000042-67208778 5'pad=0 3'pad=0 strand=+ repeatMasking=none
ATGATGGAAGGATTGAAAAAACGTACAAGGAAGGCCTTTGGAATACGGAA
GAAAGAAAAGGACACTGATTCTACAGGTTCACCAGATAGAGATGGAATTA
AGAAAAGCAATGGGGCACCAAATGGATTTTATGCGGAAATTGATTGGGAA

customProDB • 1.1k views

ADD COMMENT • link updated 6.3 years ago by xiaojing.wang ▴ 50 • written 6.4 years ago by samupatt • 0

score 0 · Answer 1 · 2018-08-07

I have updated the package on release 3.7 and devl version. On Wed, Jun 27, 2018 at 4:19 PM, samupatt [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User samupatt <https: support.bioconductor.org="" u="" 16298=""/> wrote Question: > Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table > "refGene" is not supported" <https: support.bioconductor.org="" p="" 110486=""/>: > > *Commands entered:* > > > > > library('customProDB') > > library('rtracklayer') > > session <- browserSession() > > genome(session) <- 'hg19' > > dbsnps <- trackNames(session)[grep('snp', trackNames(session), fixed=T)] > > > PrepareAnnotationRefseq(genome='hg19', CDSfasta="/home/shp12/UCSCData/refsequcsc.fasta", > pepfasta="/home/shp12/UCSCData/refpepucsc.fasta", > annotation_path="/home/shp12/Annotation_data") > > *Error obtained:* > > PrepareAnnotationRefseq(genome='hg19', CDSfasta="/home/shp12/UCSCData/refsequcsc.fasta", > pepfasta="/home/shp12/UCSCData/refpeBuild TranscriptDB object > (txdb.sqlite) ... nnotation_data") > > Error in .tablename2track(tablename, session) : > UCSC table "refGene" is not supported > > *sessionInfo()* > R version 3.4.1 (2017-06-30) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: CentOS Linux 7 (Core) > > Matrix products: default > BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.so > > 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] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] customProDB_1.18.0 BiocInstaller_1.28.0 rtracklayer_1.38.3 > [4] GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 biomaRt_2.34.2 > [7] AnnotationDbi_1.40.0 Biobase_2.38.0 IRanges_2.12.0 > [10] S4Vectors_0.16.0 BiocGenerics_0.24.0 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.17 plyr_1.8.4 > [3] compiler_3.4.1 XVector_0.18.0 > [5] GenomicFeatures_1.30.3 prettyunits_1.0.2 > [7] bitops_1.0-6 tools_3.4.1 > [9] progress_1.2.0 zlibbioc_1.24.0 > [11] digest_0.6.15 bit_1.1-14 > [13] AhoCorasickTrie_0.1.0 BSgenome_1.46.0 > [15] lattice_0.20-35 RSQLite_2.1.1 > [17] memoise_1.1.0 pkgconfig_2.0.1 > [19] rlang_0.2.1 Matrix_1.2-10 > [21] DelayedArray_0.4.1 DBI_1.0.0 > [23] GenomeInfoDbData_1.0.0 stringr_1.3.1 > [25] httr_1.3.1 Biostrings_2.46.0 > [27] hms_0.4.2 grid_3.4.1 > [29] bit64_0.9-7 R6_2.2.2 > [31] RMySQL_0.10.15 XML_3.98-1.11 > [33] BiocParallel_1.12.0 blob_1.1.1 > [35] magrittr_1.5 matrixStats_0.53.1 > [37] GenomicAlignments_1.14.2 Rsamtools_1.30.0 > [39] SummarizedExperiment_1.8.1 assertthat_0.2.0 > [41] stringi_1.2.3 RCurl_1.95-4.10 > [43] VariantAnnotation_1.24.5 crayon_1.3.4 > > > > *Head of Sequence and Peptide files in question:* > > Pep:>NP_001337147.1 > MMEGLKKRTRKAFGIRKKEKDTDSTGSPDRDGIKKSNGAPNGFYAEIDWE > RYNSPELDEEGYSIRPEEPGSTKGKHFYSSSESEEEEESHKKFNIKIKPL > QSKDILKNAATVDELKASIGNIALSPSPVRKSPRRSPGAIKRNLSSEEVA > > Seq: > >hg19_refGene_NM_001350218 range=chr1:67000042-67208778 5'pad=0 3'pad=0 > strand=+ repeatMasking=none > ATGATGGAAGGATTGAAAAAACGTACAAGGAAGGCCTTTGGAATACGGAA > GAAAGAAAAGGACACTGATTCTACAGGTTCACCAGATAGAGATGGAATTA > AGAAAAGCAATGGGGCACCAAATGGATTTTATGCGGAAATTGATTGGGAA > > > > ------------------------------ > > Post tags: customProDB > > You may reply via email or visit https://support.bioconductor. > org/p/110486/ >