"Sideloaded Area Contains No Complete CDS Feature" message during antiSMASH v7 command line job about antismash HOT 2 CLOSED

That restriction on sideloading data was added 18 months ago and has been the standard process since at least 6.1.1. It was definitely in the 7.0.0 beta version you're showing the screenshot from. Since the process should also be deterministic, I would suspect the inputs you provided have changed or aren't the same inputs as you used in the beta.

Since you're supplying a genbank file and specifying a genefinding tool, I would not be surprised if the record that fails also happens to have no genes and your chosen genefinding tool (glimmer-hmm) doesn't match up with the genefinding that DeepBGC might be doing.

If both antiSMASH and DeepBGC are able to use the same CDS annotations, or, at the very least, you're providing antiSMASH with the annotations produced by DeepBGC, then it shouldn't be a problem.

To confirm this, check if there are any CDS features annotated within the location specified in the error message. If there aren't, this is an input problem or possibly a DeepBGC problem, neither are things we can fix.
If there are CDS features present but they aren't contained, again, it's either input or DeepBGC.

If there is at least one annotated CDS feature fully contained by the subregion, then we'll need the inputs, though just the single affected record/contig will be all we need, not all 300+.

Otherwise, if you're just wanting to bypass this particular error, remove the subregion annotation from the sideloaded JSON.

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Ok. Thank you for the response. To address the inputs changing or being different, I used the exact same gbk and antismash.json as inputs for the web based beta job (that worked) and the released command line version. I have re-run DeepBGC without the ClusterFinder algorithm enabled and used that json for sideloading and it worked fine.

I am not concerned with sideloading ClusterFinder into antiSMASH and will not use that option when I want to sideload in the future. Thanks for your troubleshooting suggestions. If I have interest in sideloading ClusterFinder in the future, I will try what you have suggested. Otherwise, my issue is now resolved.

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