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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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Error regarding pygustus in singularity run #46

Closed stat-lab closed 5 months ago

stat-lab commented 5 months ago

Thank you for providing the fantastic annotation pipeline. I built the latest singularity sif container according to README, and executed the following command. singularity exec --bind $HOME,${input_file_dir} galba.sif galba.pl --genome=genome.fa --prot_seq=protein.fa --species=species3 --threads 8

Failed to execute: /opt/conda/bin/python3 ${work_dir}/GALBA/pygustus_hints.py 1> ${work_dir}/GALBA/pygustus_hints.out 2>${work_dir}/GALBA/errors/pygustus_hints.err

The content of pygustus_hints.err:

Traceback (most recent call last): File "${work_dir}/GALBA/pygustus_hints.py", line 9, in augustus.predict('/sdisk02/kosugi/C.elegans/GALBA/Cremanei_Cbriggsae/GALBA/genome.fa', species='galba_elegans4', partitionLargeSequences=True, partitionHints=True, minSplitSize=1000000, chunksize=2500000, jobs=8, **augargs) File "/opt/conda/lib/python3.10/site-packages/pygustus/augustus.py", line 42, in predict pygustus_options = util.get_options( File "/opt/conda/lib/python3.10/site-packages/pygustus/util.py", line 115, in get_options options = AugustusOptions( File "/opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py", line 87, in init self.set_value(option, value) File "/opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py", line 101, in set_value raise ValueError( ValueError: Invalid Parameter for Augustus: partitionLargeSequences

The permission of /opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py seems to be unexecutable. -rw-rw-r-- 1 root root 6591 Feb 13 22:03 /opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py

Previous issues related to this problem seems to be solved by using the latest singulrity image, but I used the latest one, and no AUGUSTUS_CONFIG_PATH is set.

It would be helpful to let me know how to solve the problem.

KatharinaHoff commented 5 months ago

Have you removed a previously existing directory ~/.augustus or $PWD/.augustus ?

On Fri, Mar 1, 2024 at 8:45 AM stat-lab @.***> wrote:

Thank you for providing the fantastic annotation pipeline. I built the latest singularity sif container according to README, and executed the following command. singularity exec --bind $HOME,${input_file_dir} galba.sif galba.pl --genome=genome.fa --prot_seq=protein.fa --species=species3 --threads 8

Failed to execute: /opt/conda/bin/python3 ${work_dir}/GALBA/pygustus_hints.py 1> ${work_dir}/GALBA/pygustus_hints.out 2>${work_dir}/GALBA/errors/pygustus_hints.err

The content of pygustus_hints.err:

Traceback (most recent call last): File "${work_dir}/GALBA/pygustus_hints.py", line 9, in augustus.predict('/sdisk02/kosugi/C.elegans/GALBA/Cremanei_Cbriggsae/GALBA/genome.fa', species='galba_elegans4', partitionLargeSequences=True, partitionHints=True, minSplitSize=1000000, chunksize=2500000, jobs=8, *augargs) File "/opt/conda/lib/python3.10/site-packages/pygustus/augustus.py", line 42, in predict pygustus_options = util.get_options( File "/opt/conda/lib/python3.10/site-packages/pygustus/util.py", line 115, in get_options options = AugustusOptions( File "/opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py", line 87, in init* self.set_value(option, value) File "/opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py", line 101, in set_value raise ValueError( ValueError: Invalid Parameter for Augustus: partitionLargeSequences

The permission of /opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py seems to be unexecutable. -rw-rw-r-- 1 root root 6591 Feb 13 22:03 /opt/conda/lib/python3.10/site-packages/pygustus/options/aug_options.py

Previous issues related to this problem seems to be solved by using the latest singulrity image, but I used the latest one, and no AUGUSTUS_CONFIG_PATH is set.

It would be helpful to let me know how to solve the problem.

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/GALBA/issues/46, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JGSA5KY5DDHPV65LGTYWAWYVAVCNFSM6AAAAABEBJQ6PGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DEOBRGY3DSNQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

stat-lab commented 5 months ago

Thank you very much for your prompt response. I successfully completed my runs after removing ~/.augustus directory that had been created for another tool, BRAKER3.

I often execute GRAKER3 with the singularity container, which also creates .augustus directory in $HOME directory. Is the ~/.augustus directory used by GALBA and BRAKER3 compatible? After running BRAKER3, can GALBA use the same ~/.augustus directory?

KatharinaHoff commented 5 months ago

The same directory can be used. Problems arise with older AUGUSTUS config files in that directory.

stat-lab @.***> schrieb am Sa. 2. März 2024 um 10:53:

Thank you very much for your prompt response. I successfully completed my runs after removing ~/.augustus directory that had been created for another tool, BRAKER3.

I often execute GRAKER3 with the singularity container, which also creates .augustus directory in $HOME directory. Is the ~/.augustus directory used by GALBA and BRAKER3 compatible? After running BRAKER3, can GALBA use the same ~/.augustus directory?

— Reply to this email directly, view it on GitHub https://github.com/Gaius-Augustus/GALBA/issues/46#issuecomment-1974749983, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JCQ34RZSNJGQVO5RPTYWGOQLAVCNFSM6AAAAABEBJQ6PGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZUG42DSOJYGM . You are receiving this because you commented.Message ID: @.***>

stat-lab commented 5 months ago

I understand. Thank you.