Hi,
Im trying to make TxDb objects for some GFF3-files of Picea abies from Congenie. Can you see any obvious reason why there are errors ? Are the GFF3 -files not compatible with the makeTxDbFromGFF or are there some updates needed ?
Kind regards
Karl
> MYBtestTxDb<-makeTxDbFromGFF("ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Trinity_kmer10.gff3.gz")
Import genomic features from the file as a GRanges object ... trying URL 'ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Trinity_kmer10.gff3.gz'
Content type 'unknown' length 13520938 bytes (12.9 MB)
==================================================
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
solving row 58427: range cannot be determined from the supplied arguments (too many NAs)
> traceback()
11: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
10: solveUserSEW0(start = start, end = end, width = width)
9: IRanges(ans_start, ans_end, names = ans_names)
8: makeGRangesFromDataFrame(df, seqnames.field = "seqid")
7: readGFFAsGRanges(con, version = version, colnames = colnames,
filter = list(type = feature.type), genome = genome, sequenceRegionsAsSeqinfo = sequenceRegionsAsSeqinfo,
speciesAsMetadata = TRUE)
6: .local(con, format, text, ...)
5: import(FileForFormat(con, format), ...)
4: import(FileForFormat(con, format), ...)
3: import(file, format = format, colnames = colnames, feature.type = GFF_FEATURE_TYPES)
2: import(file, format = format, colnames = colnames, feature.type = GFF_FEATURE_TYPES)
1: makeTxDbFromGFF("ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Trinity_kmer10.gff3.gz")
> txdB_gene2<- makeTxDbFromGFF("ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Pabies01b-gene.gff3.gz")
Import genomic features from the file as a GRanges object ... trying URL 'ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Pabies01b-gene.gff3.gz'
Content type 'unknown' length 5769965 bytes (5.5 MB)
==================================================
OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in .make_splicings(exons, cds, stop_codons) :
some CDS cannot be mapped to an exon
> traceback()
4: stop(wmsg("some CDS cannot be mapped to an exon"))
3: .make_splicings(exons, cds, stop_codons)
2: makeTxDbFromGRanges(gr, metadata = metadata)
1: makeTxDbFromGFF("ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/GFF3/Gene_Prediction_Transcript_assemblies/Pabies01b-gene.gff3.gz")
>
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.30.0 GenomicFeatures_1.32.0 AnnotationDbi_1.42.1 Biobase_2.40.0 rtracklayer_1.40.3 GenomicRanges_1.32.3
[7] GenomeInfoDb_1.16.0 IRanges_2.14.10 S4Vectors_0.18.3 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 compiler_3.5.0 XVector_0.20.0 prettyunits_1.0.2 bitops_1.0-6
[6] tools_3.5.0 zlibbioc_1.26.0 progress_1.2.0 biomaRt_2.36.1 digest_0.6.15
[11] bit_1.1-14 RSQLite_2.1.1 memoise_1.1.0 lattice_0.20-35 pkgconfig_2.0.1
[16] rlang_0.2.1 Matrix_1.2-14 DelayedArray_0.6.1 DBI_1.0.0 GenomeInfoDbData_1.1.0
[21] httr_1.3.1 stringr_1.3.1 Biostrings_2.48.0 hms_0.4.2 bit64_0.9-7
[26] grid_3.5.0 R6_2.2.2 XML_3.98-1.11 BiocParallel_1.14.1 magrittr_1.5
[31] blob_1.1.1 Rsamtools_1.32.0 matrixStats_0.53.1 GenomicAlignments_1.16.0 assertthat_0.2.0
[36] SummarizedExperiment_1.10.1 stringi_1.2.3 RCurl_1.95-4.10 crayon_1.3.4
>
did you should take a look at row 58427 as suggested in error msg? what did you see?