Closed mkardish closed 1 year ago
New pandas version - new conflicts.
I guess that you got the latest pandas version 2.0 which creates a bug in drep.
What you can do is to activate the conda env.
conda activate /p/work1/mkardish/subs/databases/conda_envs/e4ca0a910149c0c7b21c70f20a241e3d_
check the version of pandas you have.
conda list pandas
If my assumption is correct install an older version of Pandas.
conda install pandas=1.5.1
That's the version I have.
I think it's also good idea to raise the issue also at drep github and link the two issues.
Awesome! That seemed to fix the conflict. drep issue opened at : https://github.com/MrOlm/drep/issues/189
Hi Silas -- not quite sure if I should be raising this with you or on drep page, but running through the atlas pipeline I get stuck in the second step of dRep throwing an error TypeError: DataFrame.pivot() takes 1 positional argument but 4 were given. I'm currently running this stage with
atlas run genomes
On the off chance it was an install error, I deleted and reran drep in the vein of your working suggestion here https://github.com/metagenome-atlas/atlas/issues/547
But alas returned to the same error. And that was the closest similar error I was able to find. Any advice?