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

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?

About this issue

  • Original URL
  • State: open
  • Created 2 years ago
  • Comments: 40 (18 by maintainers)

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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.

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…

orf.pm file does not exist anywhere within the environment, funannotate check says all Perl dependencies are present.

alright, I’ve mamba-installed funannotate 1.8.11 (the previous available version, 1.8.12 was not available), and found orf.pm in that version 😀

~/.conda/envs/mamba/envs/funannotate1_8_11/share/glimmerhmm/train/orf.pm

The entire share/glimmerhmm directory is absent from 1.8.13 🤯 - so I’ve copied it in. I also had to replace the bin/trainGlimmerHMM script, because it was also broken in several ways 🤦🏻‍♂️

This did solve the problem, funannotate test -t predict now completes successfully!

My previous perception “conda is a nice and easy way to install pkgs with lots of dependencies” has now degraded a lot. Next time I decide to upgrade funannotate I will probably go the “build singularity from docker” route 😄