Open rpm78 opened 4 years ago
While running dbCreator with tabFile input, the following error is reported. Thanks for any advice.
> dbCreator(gtfFile=NULL,vcfFile=NULL,bedFile=NULL,tabFile=tabfile, + annotation_path=annotation_path,outfile_name=outfile_name, + genome=Rnorvegicus,outdir=outfile_path) Output novel junction peptides... Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Error in `$<-.data.frame`(`*tmp*`, "V4", value = "+") : replacement has 1 row, data has 0 > traceback() 5: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), N, nrows), domain = NA) 4: `$<-.data.frame`(`*tmp*`, "V4", value = "+") 3: `$<-`(`*tmp*`, "V4", value = "+") 2: Tab2Range(tabFile) 1: dbCreator(gtfFile = NULL, vcfFile = NULL, bedFile = NULL, tabFile = tabfile, annotation_path = annotation_path, outfile_name = outfile_name, genome = Rnorvegicus, outdir = outfile_path)
Here is the session info. I downloaded PGA from wenbostar/PGA.
wenbostar/PGA
> sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 19 Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.40.0 AnnotationDbi_1.50.0 [3] Biobase_2.48.0 BSgenome.Rnorvegicus.UCSC.rn6_1.4.1 [5] BSgenome_1.56.0 rtracklayer_1.48.0 [7] PGA_1.15.1 rTANDEM_1.27.0 [9] Rcpp_1.0.4.6 XML_3.99-0.3 [11] data.table_1.12.8 Biostrings_2.56.0 [13] XVector_0.28.0 GenomicRanges_1.40.0 [15] GenomeInfoDb_1.24.0 IRanges_2.22.2 [17] S4Vectors_0.26.1 BiocGenerics_0.34.0 [19] biomaRt_2.44.0 loaded via a namespace (and not attached): [1] httr_1.4.1 bit64_0.9-7 assertthat_0.2.1 [4] askpass_1.1 BiocFileCache_1.12.0 blob_1.2.1 [7] GenomeInfoDbData_1.2.3 Rsamtools_2.4.0 progress_1.2.2 [10] pillar_1.4.4 RSQLite_2.2.0 lattice_0.20-41 [13] glue_1.4.1 digest_0.6.25 RColorBrewer_1.1-2 [16] colorspace_1.4-1 Matrix_1.2-18 plyr_1.8.6 [19] pkgconfig_2.0.3 pheatmap_1.0.12 customProDB_1.28.0 [22] zlibbioc_1.34.0 purrr_0.3.4 scales_1.1.1 [25] processx_3.4.2 BiocParallel_1.22.0 tibble_3.0.1 [28] openssl_1.4.1 generics_0.0.2 ggplot2_3.3.1 [31] AhoCorasickTrie_0.1.0 ellipsis_0.3.1 SummarizedExperiment_1.18.1 [34] magrittr_1.5 crayon_1.3.4 memoise_1.1.0 [37] ps_1.3.3 MASS_7.3-51.6 tools_4.0.0 [40] prettyunits_1.1.1 hms_0.5.3 lifecycle_0.2.0 [43] matrixStats_0.56.0 stringr_1.4.0 munsell_0.5.0 [46] DelayedArray_0.14.0 ade4_1.7-15 compiler_4.0.0 [49] rlang_0.4.6 grid_4.0.0 RCurl_1.98-1.2 [52] rstudioapi_0.11 VariantAnnotation_1.34.0 rappdirs_0.3.1 [55] bitops_1.0-6 gtable_0.3.0 DBI_1.1.0 [58] curl_4.3 R6_2.4.1 GenomicAlignments_1.24.0 [61] Nozzle.R1_1.1-1 dplyr_1.0.0 seqinr_3.6-1 [64] bit_1.1-15.2 readr_1.3.1 stringi_1.4.6 [67] vctrs_0.3.0 dbplyr_1.4.4 tidyselect_1.1.0 >
Here is the console history
> library("biomaRt") > library("PGA") Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Biostrings Loading required package: XVector Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: data.table data.table 1.12.8 using 4 threads (see ?getDTthreads). Latest news: r-datatable.com Attaching package: ‘data.table’ The following object is masked from ‘package:GenomicRanges’: shift The following object is masked from ‘package:IRanges’: shift The following objects are masked from ‘package:S4Vectors’: first, second Loading required package: rTANDEM Loading required package: XML Loading required package: Rcpp > setwd("/home/rpm/evo/RS/PGA") > ensembl <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="rnorvegicus_gene_ensembl", + host="www.ensembl.org", path="/biomart/martservice", + archive=FALSE) Ensembl site unresponsive, trying useast mirror Ensembl site unresponsive, trying uswest mirror Ensembl site unresponsive, trying uswest mirror Ensembl site unresponsive, trying asia mirror > annotation_path <- tempdir() > PrepareAnnotationEnsembl2(mart=ensembl, annotation_path=annotation_path, + splice_matrix=TRUE, dbsnp=NULL, transcript_ids=NULL, + COSMIC=FALSE) Prepare gene/transcript/protein id mapping information (ids.RData) ... done Build TranscriptDB object (txdb.sqlite) ... Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped) Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK done Prepare exon annotation information (exon_anno.RData) ... done Prepare protein coding sequence (procodingseq.RData)... done Prepare protein sequence (proseq.RData) ... done Prepare exon splice information (splicemax.RData) ... done Warning message: In .infer_chrominfo_from_transcripts_and_splicings(transcripts$tx_chrom, : chromosome lengths and circularity flags are not available for this TxDb object > library("BSgenome.Rnorvegicus.UCSC.rn6") Loading required package: BSgenome Loading required package: rtracklayer > tabfile <- "/home/rpm/evo/RS/PGA/jum" > outfile_path<-"db/" > outfile_name<-"test" > dbCreator(gtfFile=NULL,vcfFile=NULL,bedFile=NULL,tabFile=tabfile, + annotation_path=annotation_path,outfile_name=outfile_name, + genome=Rnorvegicus,outdir=outfile_path) Output novel junction peptides... Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Error in `$<-.data.frame`(`*tmp*`, "V4", value = "+") : replacement has 1 row, data has 0 > traceback() 5: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), N, nrows), domain = NA) 4: `$<-.data.frame`(`*tmp*`, "V4", value = "+") 3: `$<-`(`*tmp*`, "V4", value = "+") 2: Tab2Range(tabFile) 1: dbCreator(gtfFile = NULL, vcfFile = NULL, bedFile = NULL, tabFile = tabfile, annotation_path = annotation_path, outfile_name = outfile_name, genome = Rnorvegicus, outdir = outfile_path)
While running dbCreator with tabFile input, the following error is reported. Thanks for any advice.
Here is the session info. I downloaded PGA from
wenbostar/PGA.Here is the console history