augustus: ERROR PP::Profile: Error parsing pattern file"/usr/local/venvs/funannotate/lib/python3.9/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8.

nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline

http://funannotate.readthedocs.io

BSD 2-Clause "Simplified" License

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augustus: ERROR PP::Profile: Error parsing pattern file"/usr/local/venvs/funannotate/lib/python3.9/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8. #973

Closed dgslos closed 8 months ago

dgslos commented 8 months ago

I keep getting:

 augustus: ERROR
        PP::Profile: Error parsing pattern file"/usr/local/venvs/funannotate/lib/python3.9/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8.

I tried installing it with sudo apt-get install augustus as suggested in #724, also tried to compile augustus 3.4 myself (got compilation errors).

I think this was solved in augustus 3.5, but this version doesn't seem to be supported by funnanotate. Can this be solved please?

Thanks in advance!

nextgenusfs commented 8 months ago

augustus v3.5 should be compatible with the latest release https://github.com/nextgenusfs/funannotate/releases/tag/v1.8.15 as well as the current master.

dgslos commented 8 months ago

Yes. I got if finally to work. I had a compilation mistake of Augustus and hence was missing some binaries. Now I can confirm it works! :)

nextgenusfs commented 8 months ago

Great, yes Augustus is a huge pain to install.....

dgslos commented 8 months ago

If someone else stumbles upon this: Compile it with 'make' and not 'make augustus' as mentioned in the wiki. Also htslib should be installed seperatly if you come across build errors mentioning htslib. https://github.com/samtools/htslib