antismash error
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12 days ago
szb6246 • 0

Hello, I have ran antismah in web and now trying to use through conda. I see that input file required is gbk. However even if we annotate fasta file with Rast or Prokka, the output is gbgff file and providing that always run into error such as

 Record c00014_NODE_14.. contains no genes and no genefinding tool specified


I have tried it with assemblies downloaded from NCBI but its same error. Can some one please guide me Command I am using is

antismash BP1199.gbff

antismash gbkfile • 354 views
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That doesn't look like an error. Probably the NODE_14 is a short contig with no genes

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11 days ago
kblin ▴ 40

You can run antiSMASH on FASTA inputs, antiSMASH will then use prodigal for gene finding. On GenBank inputs, antiSMASH will assume that you have already run gene finding yourself. As Andres mentioned, you're likely stumbling over a contig that's too small to have any genes on it. antiSMASH errors out on these when run on the command line to force you to pick a strategy for dealing with these (--genefinding-tool error). So if you just want to ignore contigs without gene calls, you could just run with --genefinding-tool none instead.

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I tried it with fasta file as well. I have assembled genomes using SPAdes. When I load them on web, I do get results but I need the output file gbk from the anti smash in command line to run the BIG-SCAPE.

How do I run antismash in command line with fasta file. Can you share the direct code please.

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Hi there, sorry for the late reply. I don't seem to get notification emails here on Biostars.

You'd run your FASTA file like:

antismash --genefinding-tool prodigal --your --other --options --here your_fasta.fa


e.g. here I'm running antiSMASH on NC_007194.fa with KnownClusterBlast, MIBiG ClusterCompare, and TIGRFam and PFAM annotations of the regions:

antismash --genefinding-tool prodigal --cb-known --cc-mibig --tigrfam --clusterhmmer NC_007194.fa