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Performance #2

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mberacochea opened this issue Feb 17, 2020 · 1 comment
Open

Performance #2

mberacochea opened this issue Feb 17, 2020 · 1 comment
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@mberacochea

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@mberacochea
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Performance bottlenecks

Currently the slowest steps are:

  • VirSorter
  • Hmmscan

Proposed solutions

hmmscan

Chunk fasta

VirSorter

There is a new version coming up in the next few weeks, wait for that release.
@mberacochea mberacochea self-assigned this Mar 6, 2020
@mberacochea mberacochea transferred this issue from another repository Apr 30, 2020
mberacochea added a commit that referenced this issue Jul 28, 2020
@mberacochea
Docker files refactor (pushed to microbiome informatics).
c5528c3 
Close for #2 and WIP for #10
@hoelzer
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hoelzer commented Feb 28, 2022

We might even go directly to VirSorter2 then instead of pushing VirSorter to a new version.

Chunking to improve speed for Hmmscan is still reasonable

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@mberacochea @hoelzer