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Gaius-Augustus / GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.
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pygustus_hints.err #41

Closed linshengnan09 closed 6 months ago

linshengnan09 commented 9 months ago

hi, I encountered an error when using GALBA for homology prediction. the err.log as follows:

ERROR in file $home/02biosoft/GALBA-1.0.8/scripts/galba.pl at line 5200 Failed to execute: $home/miniconda3/envs/GALBA/bin/python3 $home/03work/04hZ/05revio/08anno/02As/05homology_GALBA/GALBA/pygustus_hints.py 1> $home/03work/04hZ/05revio/08anno/02As/05homology_GALBA/GALBA/pygustus_hints.out 2>$home/03work/04hZ/05revio/08anno/02As/05homology_GALBA/GALBA/errors/pygustus_hints.err

pygustus_hints.err: Traceback (most recent call last): File "$home/03work/04hZ/05revio/08anno/02As/05homology_GALBA/GALBA/pygustus_hints.py", line 9, in augustus.predict('$home/03work/04hZ/05revio/08anno/02As/05homology_GALBA/GALBA/genome.fa', species='As_galba', partitionLargeSequences=True, partitionHints=True, minSplitSize=1000000, chunksize=2500000, jobs=10, **augargs) File "$home/miniconda3/envs/GALBA/lib/python3.12/site-packages/pygustus/augustus.py", line 51, in predict util.check_aug_version(augustus_command, MIN_AUG_VERSION) File "$home/miniconda3/envs/GALBA/lib/python3.12/site-packages/pygustus/util.py", line 168, in check_aug_version raise RuntimeError( RuntimeError: AUGUSTUS version 3.3.2 or higher is required!

The AUGUSTUS version I installed was 3.5.0

微信图片_20231108161207

I don't know how to solve this error. Do you have any suggestions? Thank you!

KatharinaHoff commented 9 months ago

Pygustus and Augustus are sadly a bit out of sync. We are somehow not smart enough to make sure that a parameters file ends up in the debian package of Augustus - so sorry for that. The GitHub Augustus has that file.

In the container, I patch Augustus as follows:

RUN cd /usr/share/augustus/config && \
    mkdir parameters && \
    cd parameters && \
    wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/AUG_CMDLN_PARAMETERS.md && \
    wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/aug_cmdln_parameters.json && \
    chmod a+r AUG_CMDLN_PARAMETERS.md aug_cmdln_parameters.json && \
    cd .. && \
    chmod a+r parameters && \
    chmod a+x parameters

Please check whether your Augustus has the parameters folder with these two files. If now, just add them as I do in the container.

If you obtained your Augustus from GitHub, then this will not be the cause of the problem and we need to look further.

linshengnan09 commented 9 months ago

I installed Augustus from micromamba. And I have checked the Augustus and there has the parameters folder with these two files.

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KatharinaHoff commented 6 months ago

As I said, pygustus and augustus were at some point in time out of sync. I recommend that you use your singularity container because there I make sure compatible versions are indeed used. I tested the novel container, today, and it works.

linshengnan09 commented 6 months ago

您好，您的邮件我已收到。祝生活愉快，工作顺利！