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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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problem with tbl2asn #511

Closed tivdnbos closed 4 years ago

tivdnbos commented 4 years ago

Hi,

When running prokka: prokka --metagenome --cpus 30 --outdir /my_project/prokka/COM_06/ --prefix COM_06 /my_project/megahit-output/COM_06/final.contigs.fa

It always get stuck at the tbl2asn search: Could not run command: tbl2asn -V b -a r10k -l paired-ends -M b -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z \/my_project\/prokka\/COM_06\/\/COM_06\.err -i \/my_project\/prokka\/COM_06\/\/COM_06\.fsa 2> /dev/null

Any idea how to resolve this?

Best, Tim

kapsakcj commented 4 years ago

You'll likely need to update/upgrade your tbl2asn installation since it expires. I believe the tbl2asn binary that is included with the most recent version of prokka (prokka/binaries) works with no issues.

This is a frequently encountered issue: https://github.com/tseemann/prokka/issues?q=is%3Aissue+tbl2asn

tivdnbos commented 4 years ago

Thanks! It didn´t work, but I solved it with installing the ncbi tools separately.