jeffhussmann / knock-knock

toolkit for analyzing genome editing experiments
GNU General Public License v3.0
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knock-knock paralle not working #10

Closed hukai916 closed 1 year ago

hukai916 commented 1 year ago

Hi Jeff,

I also tested the parallel commands, it pops the following error and failed to run:

knock-knock parallel test_ep300a 1 --group pacbio
Traceback (most recent call last):
  File "/opt/conda/bin/knock-knock", line 236, in <module>
    args.func(args)
  File "/opt/conda/bin/knock-knock", line 32, in parallel
    exps = knock_knock.experiment.get_all_experiments(args.project_directory, args.conditions)
  File "/opt/conda/lib/python3.10/site-packages/knock_knock/experiment.py", line 1650, in get_all_experiments
    exp = exp_class(base_dir, batch, name, description=description, progress=progress)
  File "/opt/conda/lib/python3.10/site-packages/knock_knock/experiment.py", line 139, in __init__
    features_to_show=self.target_info.features_to_show,
  File "/opt/conda/lib/python3.10/site-packages/hits/utilities.py", line 190, in memoized_f
    setattr(self, attr_name, f(self))
  File "/opt/conda/lib/python3.10/site-packages/knock_knock/experiment.py", line 206, in target_info
    supplemental_indices=self.supplemental_indices,
  File "/opt/conda/lib/python3.10/site-packages/hits/utilities.py", line 190, in memoized_f
    setattr(self, attr_name, f(self))
  File "/opt/conda/lib/python3.10/site-packages/knock_knock/experiment.py", line 194, in supplemental_indices
    return {name: locations[name] for name in self.supplemental_index_names}
TypeError: 'int' object is not iterable

Any input?

jeffhussmann commented 1 year ago

Consolidating discussion in https://github.com/jeffhussmann/knock-knock/issues/12.