problem with diamond - Githubissues

filip-husnik / pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.

GNU General Public License v3.0

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problem with diamond #44

Closed EricDeveaud closed 2 years ago

EricDeveaud commented 2 years ago

Hello

as far as I know diamond conda version is not comoiled with BLAST support.

thus pseudofinder.py ran with --diamond will fail with something like the following error message

This executable was not compiled with support for BLAST databases

one should install diamond with blast support see: see: https://github.com/bbuchfink/diamond/issues/439#issuecomment-820973039 or https://github.com/bbuchfink/diamond/wiki/2.-Installation#blast-database-support

regards

Eric

mitchso commented 2 years ago

Hi Eric,

Thank you for the heads up - it is up to the user how they would prefer to integrate diamond, using our conda environment it is possible to call diamond by providing a database with ".dmnd" suffix. Or the user could follow the installation procedures you linked.

Best, Mitch