error when creating txdb from gtf
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Last seen 3.2 years ago

I ran into an error when running the ARMOR pipeline for some RNA-seq analysis. The pipeline returns the following error, which I traced to makeTxDbFromGRanges (error pasted below). My understanding is that this is a problem caused by something wrong in the gtf file for the bacterium in question, genome annotations available here:, but I haven't been able to find the cause yet. So, if anyone has experience with what generally causes this error, it'd be much appreciated.

building TxDb with 'GenomicFeatures' package
Import genomic features from the file as a GRanges object ... 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
Calls: ... makeTxDbFromGFF -> makeTxDbFromGRanges -> .make_splicings
In addition: Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.



genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges • 887 views
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It's tough to know what is going on here without showing the code that resulted in the error. Also, ARMOR is not a Bioconductor package so you might have better luck opening an issue on the ARMOR GitHub. Then if there is indeed an issue with GenomicFeatures you can report it here or on the GitHub as an issue.


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