Open jennaj opened 1 week ago
@natefoo @mvdbeek @jennaj: tl;dr Mashmap is tricky as RAM useage depends heavily on input and parameters - 4GB - 60GB so there may be a good argument for setting boundaries on the % identity and match length to keep the RAM usage sane
Have tried a couple of sets of parameters with VGP sized inputs. The size of all the fasta matters, but a low percentage identity and a short match length will result in much, much higher RAM use.
For example, this with about 6GB of fasta @ 90% identity for 1000nt which is a relatively easy criterion to match so takes up a lot of RAM and almost 10X time:
whereas with the same fasta @ a much more stringent match requirement of 95% identity over 5000nt uses much less:
@mvdbeek: With the current
Cores Allocated 8
Memory Allocated (MB) 28672
seeing OOM failures for 1k/93% and 5k/85% (MashMap defaults) settings on typical VGP inputs. Four other combinations and inputs work fine. https://usegalaxy.org/u/fubar/h/treevalgalaugtwohaps-hg002
toolshed.g2.bx.psu.edu/repos/iuc/mashmap/mashmap/3.1.3+galaxy0
Another 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/cores at both. Maybe rolled over to higher mem at EU?