Waiting at most 5 seconds for missing files

[viksiem]

Hi, Vini

I used metaphor before and worked smoothly. But this time, with different dataset, a got this error:

Activating conda environment: ../../mambaforge-pypy3/envs/metaphor/lib/python3.11/site-packages/metaphor/config/conda/03bf6d403c24c97e82d5f2fd82f75819_ Waiting at most 5 seconds for missing files. MissingOutputException in rule DAS_tool in file /home/vik/mambaforge-pypy3/envs/metaphor/lib/python3.11/site-packages/metaphor/workflow/rules/binning.smk, line 178: Job 85 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait: output/binning/DAS_tool/cobinning/cobinning_DASTool_summary.tsv Removing output files of failed job DAS_tool since they might be corrupted: output/binning/DAS_tool/cobinning/cobinning_allBins.eval

Thanks in advance.

[vinisalazar]

Hi @viksiem,

Thank you for reporting that, and good to hear you were able to run Metaphor smoothly for your other dataset.

This could be a case where none of the bins pass DAS Tool's quality check. There are a couple of things you can try:

• rerun it and add -e "--keep-incomplete" to the command. This will prevent Snakemake from deleting the 'corrupted' output/binning/DAS_tool/cobinning/cobinning_allBins.eval file. You can then inspect this file to check your bins.
• In your metaphor_settings.yaml file, set the das_tool: score_threshold option to 0. This will disable DAS Tool's quality check, ensuring all bins pass the check.

If that is indeed the case, you will need to work with the bins resulting from MetaBAT, concoct, and vamb directly. You can do a quality-check with CheckM, and dereplicate them using dRep.

Let me know how it goes.

Vini

[viksiem]

That worked. Removing binning with vamb also worked (I still don't know why, but with metabat2 and CONCOCT runs fine).

Many thanks!

[vinisalazar]

Thank you for letting me know @viksiem. I will close this issue for now but feel free to reopen it.