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metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data
GNU General Public License v3.0
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Using diamond with SUPER-FOCUS #72

Closed linsalrob closed 2 years ago

linsalrob commented 2 years ago

There is an issue running multiple instances of SUPER-FOCUS when they are instantiated e.g. from snakemake. This PR does two things:

  1. Create a temp directory for the intermediate files to be written to
  2. Convert os.system calls to subprocess calls which are more robust and allow you to check the return code.

This PR will improve the overall stability of using diamond with SUPER-FOCUS

However, this does not completely resolve the issue with running SUPER-FOCUS using diamond on a cluster. The diamond documentation, alas, says not to do this (see How to run the program on multiple input files? on the diamond FAQ