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Better handling of mmseqs errors #111

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mmolari opened this issue Jan 21, 2025 · 2 comments · Fixed by #113
Closed

Better handling of mmseqs errors #111

mmolari opened this issue Jan 21, 2025 · 2 comments · Fixed by #113
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enhancement New feature or request

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@mmolari
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mmolari commented Jan 21, 2025

This issue is relative to the rust branch, which is not yet in production, but writing it down here to keep track of it.

On the rust branch, mmseqs alignment is currently executed by this function.
In case mmseqs command is not available in the user's path, the error message is not very immediate:

Error: 
   0: When traversing guide tree
   1: When merging graphs
   2: During self-merge iteration 0
   3: When trying to align sequences using mmseqs
   4: Running ["mmseqs" "easy-search" "/tmp/.tmpqRok4E/input.fa" "/tmp/.tmpqRok4E/input.fa" "/tmp/.tmpqRok4E/output.paf" "/tmp/.tmpqRok4E/tmp" "--threads" "1" "--max-seq-len" "10000" "-a" "--search-type" "3" "--format-output" "query,qlen,qstart,qend,empty,target,tlen,tstart,tend,nident,alnlen,bits,cigar,fident,raw" 1>"/dev/null"] failed: No such file or directory (os error 2) at packages/pangraph/src/align/mmseqs/align_with_mmseqs.rs:37

Location:
   packages/pangraph/src/align/mmseqs/align_with_mmseqs.rs:48

We could:

  • add a single preliminary check when mmseqs kernel is selected, for the availability of mmseqs command in $PATH
  • improve the handling of possible errors, similar to what done in subprocess
@mmolari mmolari added the enhancement New feature or request label Jan 21, 2025
@mmolari
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mmolari commented Jan 21, 2025

The same goes for handling of errors or missing command for minimap2-cli.

@mmolari mmolari linked a pull request Jan 22, 2025 that will close this issue
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@ivan-aksamentov
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Completed in #113

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