Request: increase memory allocation for mashmap

[jennaj]

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?

• ORG 11ac94870d0bb33a863b3f3d81b29b0a
• EU 11ac94870d0bb33ad74c8b84f6b01321

[fubar2]

@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:

[fubar2]

@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

[natefoo]

Bumped to 64GB for VGP.

[fubar2]

All 5 different sets of mashmap settings ran without drama just now - thanks @nate!
Issue resolved I think - thanks everyone!