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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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Phylophan_metagenomic's mash dist uses all cpus despite using --nproc #35

Closed jeanmanguy closed 4 years ago

jeanmanguy commented 4 years ago

Hi,

Thank you for your work.

Checking on our server with htop I realised that mash dist was using all of our CPUs. I believe it is caused by the missing -p argument here:

https://github.com/biobakery/phylophlan/blob/1b52049c7d61f0ff71e4209ae4cdd5ca2228cb4b/phylophlan/phylophlan_metagenomic.py#L513

While it is present in this call:

https://github.com/biobakery/phylophlan/blob/1b52049c7d61f0ff71e4209ae4cdd5ca2228cb4b/phylophlan/phylophlan_metagenomic.py#L554

fasnicar commented 4 years ago

Hi, many thanks for reporting this. I explicitly added '-p', '1' to line 513 with commit 2378603a52e0b6e86cd87c47a848b3362bab32a9. Can I ask you which version of mash you're running? In the old versions, the default was 1 if not specified, but that might be changed in a new release.

Many thanks, Francesco

jeanmanguy commented 4 years ago

Wonderful, thank you Francesco!

I am running phylophlan (3.0.31) and mash (2.2.2) out of bioconda. Yes I think I had the same issue when trying to use Mash for another project earlier this year, it feels like a familiar problem I had. At least we can use -p, that's weird though.