search

faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
Other
78 stars 49 forks source link

phyluce_assembly_assemblo_spades memory allocation issue on cluster #257

Open mprebus opened 2 years ago

mprebus commented 2 years ago

I've been having some issues lately trying to run assemblies on our cluster with phyluce-1.7.1. Specifically, assembly fails on several samples, and inspection of the spades.log reveals:

: Error in malloc(): out of memory Requested: 34816 Increasing RAM doesn't fix the problem though. This seems to be a common complaint about SPAdes, and apparently is linked to how it interacts with some common Linux operating systems, e.g. https://github.com/ablab/spades/issues/494 Has anyone else run into this problem? Supposedly SPAdes 3.15 addresses this issue.
brantfaircloth commented 2 years ago

Although I am not sure that the updated spades fixes the issues (from reading the thread linked), you could try a couple of things:

  1. if you've used conda, you could conda update spades=3.15.2. That should update the spades binaries/scripts that phyluce uses to the newer version - and then you can try assembling again.
  2. you could compile spades on the machine/cluster you are using and update it's location by changing the path within the phyluce config file. This file is normally in $CONDA/envs/phyluce-1.7.1/phyluce/config/phyluce.conf where $CONDA is the directory of your conda install. Then reassemble. (edited to finish thought...)
mprebus commented 2 years ago

Thank you! I updated SPAdes to the latest version using conda update spades. I'll let you know how it goes.

mprebus commented 2 years ago

This fixed the issue on our cluster (which is running CentOS 7.9.2009).

brantfaircloth commented 2 years ago

Excellent.