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a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
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LAsort fails in dailgner2.0 #5

Closed a-ludi closed 4 years ago

a-ludi commented 4 years ago

Hi Arne,

The LAsort and LAmerge calls seem to have a bit of a problem if I use them from the daligner that I installed from git. Notice the “.N@” that gets appended. However, the LAsort and LAmerge from conda seem to work fine. However, the LAcheck from conda fails the “ref_vs_reads_alignment_block” because it tries to append “.las” to the second argument. The LAcheck from the daligner that I installed from git does work fine though.

daligner2.0: Command Failed: LAsort /mnt/shared_tmp/376067.1.work.q/daligner.7314/scaffolds_FINAL.1.scaffolds_FINAL.7.N@

So, the furthest that we’ve progressed is with local damapper and LAcheck. The other prerequisites are from conda.

Originally posted by @BradleyRan in https://github.com/a-ludi/dentist/issues/3#issuecomment-632727668

a-ludi commented 4 years ago

Hi Randy,

could you please verify you are running the same version of LAsort, LAmerge and daligner by typing

which LAsort LAmerge daligner

The output should look something like this

$ which LAsort LAmerge daligner
/home/alu/.local/bin/LAsort
/home/alu/.local/bin/LAmerge
/home/alu/.local/bin/daligner

The @ notation was introduced in 2018 and the bioconda version of daligner is ancient (2015). So, maybe daligner calls the bioconda version of LAsort by accident. I never had this issue myself, so it is very unlikely that it is a bug in DALIGNER.

a-ludi commented 4 years ago

This issue is related to a new feature in LAsort see issues #7. As a quick fix, use LAsort as of 2020-01-15.