Request: increase memory allocation for miniprot

galaxyproject / usegalaxy-tools

usegalaxy.* common tools

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Request: increase memory allocation for miniprot #832

Open jennaj opened 2 months ago

jennaj commented 2 months ago

toolshed.g2.bx.psu.edu/repos/iuc/miniprot/miniprot/0.13+galaxy0

Example job from Ross @fubar2 that fails at ORG but runs Ok at EU (same inputs/params/tool version). Seems to have similar default mem at both. Maybe rolled over to higher mem at EU?

ORG bbd44e69cb8906b5091a756127dc6830 (60384790)
EU 11ac94870d0bb33a8840cfccb3e14c6f

fubar2 commented 1 month ago

@natefoo @mvdbeek @jennaj: More pictures and numbers to help figure out what this tool needs.

Manually ran Miniprot2 on the NCBI human protein fasta - that's what VGP needs it for.

Briefly uses about 22GB then bounces around 8-12GB It used 4 threads without being told.

fubar2 commented 1 month ago

Just reran miniprot on an NCBI protein fasta at @jennaj request - failed OOM - bug report sent. What's really odd is this at submission - saying the job invocation failed - although the job 19 is yellow in this screen grab:

natefoo commented 1 month ago

Bumped to 28 GB.

fubar2 commented 1 month ago

@natefoo: worked fine just now on a typical NCBI protein fasta - thanks everyone! Issue seems to be resolved.