Tool: Funannotate Predict (Galaxy Version 1.8.17+galaxyX)
Server OS: Debian GNU/Linux 12
Python: 3.11.13
Goal: Annotating fungal genome (Hyphopichia burtonii) using soft-masked genome from BRAKER3, protein evidence (no RNA-seq).
Job log excerpt:
…
[Aug 15 03:52 PM]: Running Augustus gene prediction using hyphopichia_burtonii_y951 parameters
Traceback (most recent call last):
File “/usr/local/bin/funannotate”, line 10, in
sys.exit(main())
File “/usr/local/lib/python3.11/site-packages/funannotate/funannotate.py”, line 717, in main
mod.main(arguments)
File “/usr/local/lib/python3.11/site-packages/funannotate/predict.py”, line 2156, in main
subprocess.call(cmd)
File “/usr/local/lib/python3.11/subprocess.py”, line 389, in call
with Popen(*popenargs, **kwargs) as p:
File “/usr/local/lib/python3.11/subprocess.py”, line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File “/usr/local/lib/python3.11/subprocess.py”, line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: ‘/usr/local/lib/python3.11/site-packages/funannotate/aux_scripts/augustus_parallel.py’
It seems augustus_parallel.py in the funannotate aux_scripts folder is not executable on the server, so the tool cannot run Augustus in parallel mode.
Questions:
Could the permissions on augustus_parallel.py be fixed on the Galaxy instance?
Is there a workaround (e.g., disable parallel Augustus or run with single core) while waiting for a fix?
Yes, there does seem to be a problem with the job execution.
Does this same error come up with different samples and parameter choices? Has this tool ever worked? This same version or earlier versions? You could try running the tool test data as a simple baseline. The test is just to eliminate the actual root error from being due to something else. Then if the tool test also fails, continue on..
I’m assuming this is a server you are administrating. You could try installing the tool again and choosing to use the “manage dependencies” option. This can be a bit easier than attempting to get all of those together manually. Try this installation next, then the tool test again, then your other sample.
Yes, I’ve recently worked with a similar dataset and had a positive experience. I used Funannotate Predict and Funannotate Functional to annotate my yeast genome. I was able to select the lineage Saccharomycetes and specifically Saccharomyces for gene prediction, and under BUSCO, I also selected the correct lineage to ensure accurate benchmarking. The annotation was performed on the same dataset just last month, and the tools ran smoothly, providing reliable gene models and functional annotations.
Thanks for following up. I was able to reproduce the error this morning at the EU server, and we had a report of a problem at the ORG server I can reproduce.
Thanks for following up! I wasn’t sure if you were actually working at the UseGalaxy.eu server or not but now I am guessing that you are? A tool issue in the runtime environment was unexpected at the public sites but let’s see what the developers have to say.
I’m putting the workaround at the top so others can find it.
Thanks for the update and for reproducing the error. Yes, I am working on the UseGalaxy.eu server, so that makes sense. I appreciate you creating a ticket and providing a workaround—it’s very helpful. I’ll keep an eye on the GitHub issue for any updates from the developers.
