Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Not recognizing BUSCO? #236

Open
incoreygible opened this issue Feb 2, 2022 · 0 comments
Open

Not recognizing BUSCO? #236

incoreygible opened this issue Feb 2, 2022 · 0 comments

Comments

@incoreygible
Copy link

I have BUSCOv5.2.2 installed via conda and the metazoa busco database included in the database folder I point to with --database-dir. When attempting to execute the annotate step, it looks like dammit is not recognizing busco:

Traceback (most recent call last):
  File "/data1/rennolds/miniconda3/bin/dammit", line 9, in <module>
    sys.exit(app.DammitApp(arg_src=sys.argv[1:]).run())
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/app.py", line 45, in run
    return self.args.func()
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/app.py", line 333, in handle_annotate
    build_default_pipeline(annotate_handler,
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/annotate.py", line 133, in build_default_pipeline
    register_busco_task(handler, config, databases)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/annotate.py", line 245, in register_busco_task
    task = BuscoTask().task(input_fn,
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/utils.py", line 89, in d_to_t
    task_dict = task_dict_func(*args, **kwargs)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/profile.py", line 163, in func
    task = task_func(*args, **kwargs)
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/tasks/busco.py", line 61, in task
    exc = self.deps()
  File "/data1/rennolds/miniconda3/lib/python3.9/site-packages/dammit/tasks/busco.py", line 29, in deps
    raise InstallationError('BUSCO not found. NOTE: '\
dammit.tasks.utils.InstallationError: BUSCO not found. NOTE: dammit 1.0 requires BUSCO v2 or greater

I definitely have Busco v2 or greater. I am using the most recent version of dammit. Any idea how to fix this?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant