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KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
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No markers found - attempts made to find/count kmers #237

Closed samche42 closed 2 years ago

samche42 commented 2 years ago

Issue: If markers can't be found for a specific dataset, it skips the dataset (awesome). However, it seems that the program still tries to find kmers from the datasets in the next step and then fails.

I had five of what I call "naughty" datasets where no markers could be found. They were ignored but then Autometa fell on its face during the kmer step. I removed those datasets from the sample sheet and re-ran it. Autometa ran perfectly with the remaining two datasets.

Suggested fix: Datasets with no markers should be ignored in all downstream processes and reported as failed at the end. Datasets that are ok should be allowed to complete.

evanroyrees commented 2 years ago

Can you also place some example error output here for context/testing/troubleshooting?

samche42 commented 2 years ago

You can go ahead and remove this issue. I updated Autometa (I.e. replaced my nf-core env with the autometa-nf env) and couldn't recreate the problem. Assuming I just had an old bit of code floating around somewhere :)