Fail if Bedtools issues a fasta normalization error

[jdwinkler-lanzatech]

Hi,

I've been digging into why --outseq has been generating empty sequence files despite there being results in the Barrnap generated GFF files. It looks like Bedtools is rejecting some of my assemblies due to different line lengths for some parts of the sequence. It would be nice if Barrnap failed if this happened, as the exit code for Barrnap is currently 0 even if outseq fails.

Let me know if my description isn't clear, happy to add more detail as needed.