nextgenusfs
commented
3 years ago Downgrade Augustus -- in the newest version they changed something and output is failing in BUSCO. So anything < 3.4 should work.
Closed rpetit3 closed 3 years ago
nextgenusfs
commented
3 years ago Downgrade Augustus -- in the newest version they changed something and output is failing in BUSCO. So anything < 3.4 should work.
rpetit3
commented
3 years ago Great! I'll give it a go. Want me to update the Conda recipe to pin Augustus to be <3.4?
rpetit3
commented
3 years ago The downgrade on Augustus worked. Got another error, but I think its related to GeneMark. I'm getting a segmentation fault, but reached out to GaTech folks to hopefully get a working binary.
Does this look like an error that broken GeneMark binary would cause?
#########################################################
SUCCESS: `funannotate predict` BUSCO-mediated training test complete.
#########################################################
Now running predict using all pre-trained ab-initio predictors
CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate2 --cpus 8 --species Awesome busco -p annotate/predict_results/awesome_busco.parameters.json
#########################################################
-------------------------------------------------------
[01:22 AM]: OS: Debian GNU/Linux 10, 24 cores, ~ 264 GB RAM. Python: 3.8.6
[01:22 AM]: Running funannotate v1.8.3
[01:22 AM]: Ab initio training parameters file passed: annotate/predict_results/awesome_busco.parameters.json
Traceback (most recent call last):
File "/home/rpetit3/miniconda3/envs/funannotate/bin/funannotate", line 713, in <module>
main()
File "/home/rpetit3/miniconda3/envs/funannotate/bin/funannotate", line 703, in main
mod.main(arguments)
File "/home/rpetit3/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 499, in main
shutil.copyfile(trainingData['genemark'][0]['path'], os.path.join(
File "/home/rpetit3/miniconda3/envs/funannotate/lib/python3.8/shutil.py", line 261, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/home/rpetit3/test-genemark/test-busco_4169/annotate/predict_misc/ab_initio_parameters/awesome_busco.genemark.mod'
#########################################################
Traceback (most recent call last):
File "/home/rpetit3/miniconda3/envs/funannotate/bin/funannotate", line 713, in <module>
main()
File "/home/rpetit3/miniconda3/envs/funannotate/bin/funannotate", line 703, in main
mod.main(arguments)
File "/home/rpetit3/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 406, in main
runBuscoTest(args)
File "/home/rpetit3/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 217, in runBuscoTest
assert 1500 <= countGFFgenes(os.path.join(
File "/home/rpetit3/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 44, in countGFFgenes
with open(input, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: 'test-busco_4169/annotate2/predict_results/Awesome_busco.gff3'`If you could update conda recipe that would be awesome.
Second error possible if genemark failed in the first go than the json parameter file could have been pointing to a None or empty file.
rpetit3
commented
3 years ago I'll update the recipe.
And yeah, I agree its probably GeneMark.
I'll close this for now, thanks for the help Jon!
Are you using the latest release? Yep (I think)! Installed through Conda
Describe the bug I ran the test set, and I got the following error:
This might be related to https://github.com/nextgenusfs/funannotate/issues/418 (tblastn exiting earliy), but there isn't a way to set
--min_training_models. I'm trying a rerun with 1 cpu to rule out multithreaded tblastn causing BUSCO to exit early. Will let you know if it succeeds or not.What command did you issue?
Logfiles
funannotate check output
OS/Install Information OS info:
Versions info