Error in GenomicFeatures::extractTranscriptSeqs(x = genome, transcripts = grl) :
some transcripts in 'transcripts' are on chromosomes that are not in
'x' (e.g. some transcripts are on chromosome "CHR_MG117_PATCH" but this
chromosome is not in 'x')
Calls: extractTxSeqs -> <Anonymous> -> <Anonymous>
In addition: Warning messages:
1: In call_fun_in_txdbmaker("makeTxDbFromGFF", ...) :
makeTxDbFromGFF() has moved to the txdbmaker package. Please call
txdbmaker::makeTxDbFromGFF() to get rid of this warning.
2: 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.
Execution halted
createIndices