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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
The text was updated successfully, but these errors were encountered:
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:We could:
mmseqs
command in $PATHThe text was updated successfully, but these errors were encountered: