nullarbor

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I'm getting the complaint:

[00:57:44] Contig ID must <= 20 chars long: gnl|X|SRR1207440_contig000001
[00:57:44] Please rename your contigs or use --centre XXX to generate clean contig names.

Any tips on how to either pass the --centre XXX argument via nullarbor, change the nullarbor configuration, or perhaps sed -i something in one of the files?

i've also just brew install nullarbor --HEAD and brew install prokka --HEAD and still get the same issues. it looks like prokka is using the --compliant option. in the Makefile generated by nullarbor:

SRR1207440/prokka/SRR1207440.gff: SRR1207440/contigs.fa
    prokka --centre X --compliant --force --fast --locustag SRR1207440 --prefix SRR1207440 --outdir SRR1207440/prokka --cpus $(CPUS) $^

and the prokka error logs are showing:

[00:41:31] Loading and checking input file: SRR1207440/contigs.fa
[00:41:31] Contig ID must <= 20 chars long: gnl|X|SRR1207440_contig000001
[00:41:31] Please rename your contigs or use --centre XXX to generate clean contig names.

This hack seems to help. With the nullarbor Makefile:

sed -i 's/locustag SRR[0-9]*/locustag x/g' Makefile