augustus: ERROR PP::Profile: Error parsing pattern file

See original GitHub issue

I’m using the latest Funnanotate, but when I reach the “funannotate predict” step I get this:

augustus: ERROR
        PP::Profile: Error parsing pattern file"/sw/anaconda/2019.10/envs/funannotate-test/lib/python3.8/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8.
[May 18 12:01 PM]: ERROR: augustus --proteinprofile test failed, likely a compilation error. This is required to run BUSCO, exiting.

(conda env is called funannotate-test)

which Augustus give me: /sw/anaconda/2019.10/envs/funannotate-test/bin/augustus So I think it’s looking at the right Augustus. I tried updating Augustus, but

Updating augustus is constricted by
/ funannotate -> requires augustus==3.3.3=pl5262h5a9fe7b_6

"

So I did a “conda install augustus==3.3.3=pl5262h5a9fe7b_6 --force-reinstall” just in case, but the error persists. (curiously I have another instance of funannotate running and it worked despite some augustus errors. Also, maybe it’s worth noting, that I re-installed it fresh on this new conda environment because it was the only way to go around a “Diamond repeat database was created with different version of diamond, please re-run funannotate setup” error message that never disappeared no matter what I did.)

Any suggestions?

Issue Analytics

  • State:open
  • Created a year ago
  • Comments:40 (18 by maintainers)

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1reaction
nextgenusfscommented, Aug 26, 2022

In the docker build I just used the version in apt-get which is functional, so if you are on Debian that is the quickest solution. On my Mac I was able to build the latest source code from Augustus repo and that also worked.

1reaction
nextgenusfscommented, Aug 24, 2022

So once you have a working environment you should mostly be able to just upgrade funannotate with pip in that environment. I have love/hate view if conda as well…

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