Could not locate command line parameters file

[LandiMi2]

Trying to run predict step. Augustus is well setup but I get an error:

augustus: ERROR Could not locate command line parameters file: /data01/mlandi/TME117-assembly/funannotate/new-sept/train/fun/predict_misc/ab_initio_parameters/augustus/parameters/aug_cmdln_parameters.json.

that I don't seem to understand. @nextgenusfs . The folder parameter is not present, I don't know how to fix this

[LandiMi2]

more specifically here is a screen shot

[nextgenusfs]

What version of Augustus? This must be that "new" parameters file required by Augustus. So we need to figure out where this file lives in the default Augustus species folders and have it copied over to the local working directory, at least that is what it seems.

[LandiMi2]

I am using AUGUSTUS (3.4.0). The augustus species folder is created ..../predict_misc/ab_initio_parameters/augustus. This folder for now has: extinisic/ model/ profile/ species - no parameters folder

[nextgenusfs]

Try to upgrade to latest in repo via pip and see if that works, ie from your environment:

python -m pip install git+https://github.com/nextgenusfs/funannotate.git --upgrade --force --no-deps

[LandiMi2]

Okay great! I am re-running the step. I will get back to you. The upgrade is done

[LandiMi2]

previous error solved ."Manihot" is my species

[nextgenusfs]

Okay, you have the rest of the log file and let me know what files are in .../fun/predict_misc/ab_initio_parameters/augustus/species/manihot_esculenta? Seems either like training didn't complete properly or v3.4 requires some additional files that previous versions do not need.

[nextgenusfs]

Eek. Took me awhile, but I think I might finally have v3.4 compiled locally, so I'll try to replicate. Nevermind, still struggling to get v3.4 installed to test.

[LandiMi2]

Sorry, when I replied it was midnight. here is the list of mahihot directory

[LandiMi2]

@nextgenusfs thanks for this!! Did you manage testing v3.4?

[LandiMi2]

@nextgenusfs any breakthrows?

[nextgenusfs]

I was unable to install working version of Augustus 3.4 so unable to test locally. I will have to try docker. How about the logfile? Any errors of note in there for the training steps?

[LandiMi2]

@nextgenusfs training step worked okay till the end. It's just the Augustus in predict that throws an error

[LandiMi2]

Does Augustus v3.3.2 work okay? with the folders?

[nextgenusfs]

Sorry for delayed response (day job caught up with me ;). But yes versions <3.4 should work fine. I have not been able to get a working version of v3.4 in order to test -- however, it seems that a pptx bug was just fixed upstream so maybe I can get it working now -- just need to find some time to give it a try. But fastest resolution would be to downgrade to v3.3.2.

[LandiMi2]

okay, thanks. Do tell once you have it running for version 3.4

[vflorelo]

I got my funannotate installation working with augustus 3.5.0 I edited the predict.py file, I don't have the original line numbers but, just below this block of code:

lib.copyDirectory(os.path.join(FUNDB, 'trained_species', args.busco_seed_species), os.path.join(LOCALAUGUSTUS, 'species', args.busco_seed_species), overwrite=True)
lib.copyDirectory(os.path.join(FUNDB, 'trained_species', 'anidulans'), os.path.join(LOCALAUGUSTUS, 'species', 'anidulans'), overwrite=True)
lib.copyDirectory(os.path.join(AUGUSTUS, 'species', 'generic'), os.path.join(LOCALAUGUSTUS, 'species', 'generic'), overwrite=True)
lib.copyDirectory(os.path.join(AUGUSTUS, 'extrinsic'), os.path.join(LOCALAUGUSTUS, 'extrinsic'), overwrite=True)
lib.copyDirectory(os.path.join(AUGUSTUS, 'model'), os.path.join(LOCALAUGUSTUS, 'model'), overwrite=True)
lib.copyDirectory(os.path.join(AUGUSTUS, 'profile'), os.path.join(LOCALAUGUSTUS, 'profile'), overwrite=True)

You need to add the following line:

lib.copyDirectory(os.path.join(AUGUSTUS, 'parameters'), os.path.join(LOCALAUGUSTUS, 'parameters'), overwrite=True)

And voila, funannotate running without a hassle with augustus 3.5