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:https://www.ncbi.nlm.nih.gov/assembly/GCF_002277975.1, 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.
Error: 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.