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dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.
MIT License
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error during predict-translated-orfs step #99

Closed jogmiers closed 5 years ago

jogmiers commented 5 years ago

Hello,

I am able to run prepare-rpbp-genome and create-orf-profiles just fine, with both the sample data and with my data. However, when I go to run predict-translated-orfs, I get the following Python error; I get the same error both with the sample data and with my data:

Screen Shot 2019-06-06 at 5 29 22 PM

I am pretty new to Python, and I am at a loss as to what's generating this error. Any help would be much appreciated.

eboileau commented 5 years ago

Hi,

joblib has changed it's default backend from multiprocessing to loky since version 0.12, and this is the cause of this error. I have fixed this in the development branch, however I am working on other issues now, and there will be a change in API. If you can wait a couple of days, say next Tuesday, I think I should be able to push a working version. Otherwise, if you pip install joblib==0.11, this should go back to the old backend.

jogmiers commented 5 years ago

thank you

eboileau commented 5 years ago

The current dev branch should be working. Inside the rp-bp project directory, you can git checkout dev, and git pull, then follow the latest instructions for installation here. You can also recompile the Stan models.

I'll be updating the analysis scripts (post-processing) soon, etc. so I would advise to pull regularly and reinstall to get the latest changes.