Error: One or more diamond tasks failed to run

[OPeterJ]

Hi Stephen,
Thanks for your pipeline of human gut viruses classification.
I was trying to use the uhgv-tools to classifiy viral contigs, but I met one error when I repeat the test dataset.

The error information as follow:
Error: One or more diamond tasks failed to run
See logs for details: output/tmp/selfaln/*.log

The details in log:
No such file or directory
Error: Error opening file output/tmp/selfaln/1.faa.dmnd
No such file or directory
Error: Error opening file output/tmp/selfaln/2.faa.dmnd
No such file or directory
Error: Error opening file output/tmp/selfaln/3.faa.dmnd
No such file or directory
Error: Error opening file output/tmp/selfaln/4.faa.dmnd
No such file or directory
Error: Error opening file output/tmp/selfaln/5.faa.dmnd

Thank you very much for your help.
Best,
Peter

[snayfach]

Thanks - I'll have a look at this later in the week. In the meantime, I've seen this occur when the diamond database is incompatible with the installed version. You may try to rebuild and replace the diamond database.

[snayfach]

Sorry for the delay -- were you able to resolve the issue? Can you send me a compressed tarball of the full output?

[snayfach]

Thank you -- I tracked down the issue to the version of DIAMOND. If you revert to V2.1.8 the issue should be resolved:

conda install -c bioconda diamond=2.1.8

[OPeterJ]

Thanks for your reply, I have resolved the issue with editing the classify.py file (lines 314-315). I also tried with diamond v2.1.8, but it seemed not work.
314 cmd = f"diamond makedb --in {path} --db {path} 1>{path}.dmnd.log 2>&1 && " #add this line
315 cmd += "diamond blastp " #change = to +=
The output of test data and the edited classify.py file have been send to you with e-mail.
Best,
Peter

[snayfach]

Glad you found a solution. My guess is you built the diamond database using v2.1.9 (vis the download module), then downgraded to v2.1.8. This issue should be fixed when a new diamond version is released. If others encounter this issue, try rerunning the uhgv-tools download . command after downgrading DIAMOND to v2.1.8

[OPeterJ]

Thanks a lot！