Progressing despite individual binner failure

[mladen5000]

• [ x] I checked and didn't found a related issue,e.g. while typing the title
• [x] I got an error in the following rule(s):

• [ x] I checked the log files indicated indicated in the error message (and the cluster logs if submitted to a cluster)

Here is the relevant log output:

My issue pertains to binning -> genome creation. I often have smaller datasets so I am interested in performing ensemble binning [metabat, maxbin, vamb, and semibin], however, many times there are 1,2, even 8 samples that don't recover bins. It seems if using das tool this should be ok. Instead I typically resort to attempting all 4 methods but almost always am required to stick to metabat as the final binner.

Perhaps touching a temp file (results header, just empty for example) when binning is complete is possible?

Atlas version 2.16.1 Additional context Add any other context about the problem here.

[SilasK]

Can you tell me which binner you used? maxbin?

Would you be ok to simply not bin this sample?

You could still use it to be quantified..

[mladen5000]

I used initially wanted to use all 4 available and aggregate with DASTools. Maxbin however is the one where this most frequently occurs. I think the most convienent option would be to have the workflow continue without having to manually curate the config and samples (Currently I end up removing maxbin, then removing either vamb or Semibin if they cause issues, then switching the final binner to metabat, and finally dropping samples from samples.tsv).

If there's a way to not bin but still quantify that would be great

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