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Progressing despite individual binner failure #651

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mladen5000 opened this issue May 13, 2023 · 3 comments
Open
1 task done

Progressing despite individual binner failure #651

mladen5000 opened this issue May 13, 2023 · 3 comments

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@mladen5000
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mladen5000 commented May 13, 2023

  • [ x] I checked and didn't found a related issue,e.g. while typing the title
  • ** 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
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@SilasK
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SilasK commented May 15, 2023

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
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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

@github-actions github-actions bot added the stale label Jul 15, 2023
@metagenome-atlas metagenome-atlas deleted a comment from github-actions bot Jul 15, 2023
@github-actions github-actions bot added the stale label Sep 14, 2023
@metagenome-atlas metagenome-atlas deleted a comment from github-actions bot Sep 15, 2023
@github-actions github-actions bot removed the stale label Sep 15, 2023
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There was no activity since some time. I hope your issue is solved in the mean time.
This issue will automatically close soon if no further activity occurs.

Thank you for your contributions.

@github-actions github-actions bot added the stale label Nov 14, 2023
@github-actions github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Nov 30, 2023
@SilasK SilasK added keep and removed stale labels Nov 30, 2023
@SilasK SilasK reopened this Nov 30, 2023
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