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.
> 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
>
> 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