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Check FASTA sequences:
- Ensure terminal EOL (so concatenation works) – dos2unix, or append "\n"
- Ensure sequence uses nucleotide alphabet? – seqkit or biopython; see minimap2 input requirements
Check BED versus FASTA sequences (currently handled but roundabout):
- "vector" contig name from annotation BED matches contig name in the vector FASTA
- "repcap" contig name from annotation BED matches one contig name in either the vector FASTA or packaging FASTA
- "vector" contig name is not used in packaging or host FASTA files
- Contig names are not reused between packaging and host FASTA files
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