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bonsai-team / matam

Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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Makes all read counting dependent on args.verbose #112

Closed tazend closed 1 year ago

tazend commented 1 year ago

On our HPC Cluster with a shared networked filesystem and 1000+ matam jobs running at the same time our filesystem was saturated due to the many wc -l subprocesses.

By looking at the matam_assembly.py script we realized that all the read counting done with wc -l is only used for logging purposes and does not actually affect any computation. That's why we decided to make it optional based on args.verbose.

wookietreiber commented 1 year ago

Thanks for merging and releasing this quickly! Do you have an estimate on when the new release will be up on conda?

ppericard commented 1 year ago

The bioconda bot should pick up the release automatically within a few hours/days. I will submit a manual update if it has not been done soon. P.

ppericard commented 1 year ago

@wookietreiber, quick update. The Continuous Integration pipeline for Bioconda is currently broken, preventing most tools from being updated. The pull request (https://github.com/bioconda/bioconda-recipes/pull/40054) only needs to be validated by the CI once it starts working again, and this new version of MATAM should be online.

ppericard commented 1 year ago

MATAM v1.6.1 is now live on bioconda !