I'm having troubles with ensDbFromGtf for some gtf files downloaded from Ensembl ftp. I want to use maize gtffile to get a EnsDb, but Can not get the sequence lengths from Ensembl or Ensemblgenomes.code show as below：
gtffile <- "..\\Zea_mays.AGPv4.36.gtf"
and I get some warning messages：
Warning messages:
1: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, :
I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty!
2: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, :
I'm missing column(s): 'transcript_name'. The corresponding database columns will be empty!
3: In .getSeqlengthsFromMysqlFolder(organism = organism, ensembl = ensemblVersion, :
Can not get the sequence lengths from Ensembl or Ensemblgenomes. Seqinfo will lack the sequence lengths.
4: In tryGetSeqinfoFromEnsembl(organism, version, seqnames = chroms$seq_name) :
Unable to retrieve sequence lengths from Ensembl.
5: In UseMethod("seq") :
closing unused connection 4 (ftp://ftp.ensemblgenomes.org/pub/release-36/bacteria/mysql/)
6: In UseMethod("seq") :
closing unused connection 3 (ftp://ftp.ensembl.org/pub/release-36/mysql/)
DB <- ensDbFromGtf(gtf =gtffile)EDB <- EnsDb(DB)annotations <- GetGRangesFromEnsDb(EDB)
Error in asMethod(object) :
cannot create a GRanges object from a Seqinfo object with NA seqlengths
I'm having troubles with ensDbFromGtf for some gtf files downloaded from Ensembl ftp. I want to use maize gtffile to get a EnsDb, but Can not get the sequence lengths from Ensembl or Ensemblgenomes.code show as below：
gtffile <- "..\\Zea_mays.AGPv4.36.gtf"and I get some warning messages：Warning messages: 1: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, : I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty! 2: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, : I'm missing column(s): 'transcript_name'. The corresponding database columns will be empty! 3: In .getSeqlengthsFromMysqlFolder(organism = organism, ensembl = ensemblVersion, : Can not get the sequence lengths from Ensembl or Ensemblgenomes. Seqinfo will lack the sequence lengths. 4: In tryGetSeqinfoFromEnsembl(organism, version, seqnames = chroms$seq_name) : Unable to retrieve sequence lengths from Ensembl. 5: In UseMethod("seq") : closing unused connection 4 (ftp://ftp.ensemblgenomes.org/pub/release-36/bacteria/mysql/) 6: In UseMethod("seq") : closing unused connection 3 (ftp://ftp.ensembl.org/pub/release-36/mysql/)
DB <- ensDbFromGtf(gtf =gtffile)EDB <- EnsDb(DB)annotations <- GetGRangesFromEnsDb(EDB)Error in asMethod(object) : cannot create a GRanges object from a Seqinfo object with NA seqlengths