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filip-husnik / pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.
GNU General Public License v3.0
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Pseudofinder sleuth is stuck on psl2aln #48

Closed tandb92 closed 2 years ago

tandb92 commented 2 years ago

When I run pseufonder.py sleuth, the terminal stuck on pal2aln and does not move for over 30 minutes. What can i do?

mitchso commented 2 years ago

Hi,

This is an issue with pal2nal itself and we are working on a workaround - the issue is that when the pathnames provided to pal2nal are too long, it hangs. You should be able to resolve this by providing shorter pathnames to pseudofinder. If you are calling sleuth directly, you should specifically shorten whatever you are providing to the the --outdir flag. If you are calling within annotate, make sure that --output_prefix is not too long.

Hopefully this helps!