error orig_shape, "Dimension mismatch"

[Ajeet1699]

Hi,

I am trying to run the ABC snakemake pipeline, and is giving me the error.

ABC-Enhancer-Gene-Prediction-1.1.2/workflow/scripts/neighborhoods.py", line 577, in count_single_feature_for_bed
assert df.shape[0] == orig_shape, "Dimension mismatch"
^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Dimension mismatch

Any help for this error?

Thanks

[mayasheth]

Hi, it seems like others have encountered this error in the past due to package version issues. Can you confirm that you are using the main branch and the specified conda environment? Also try removing the previous output files for this sample before rerunning in case these are incomplete for some reason.

Let me know if either of these helps!

[Ajeet1699]

Hi,
Thanks for quick response. I was using the v1.1.2. I am running again now with main branch.
I will let you know if any error occurs or completed successfully :)

Thanks

[Ajeet1699]

Hi,
Same error occurs using main branch in specified conda env. I have also deleted the previous output.

[mayasheth]

Hmm, looking at previous issues that report this error, it seems to be an issue with rows being dropped when merging in line 575 of neighborhoods.py. Could you try:

1. Comparing the dimension of the dataframe before and after the merging in line 575?
2. Running the pipeline with this line commented out?

In the mean time, we will look into resolving this error more permanently.

[Ajeet1699]

Hi, I have compared the dimension of the dataframe before and after the merging in line 575. It was equal, and also unequal for various samples. By commenting the line, pipeline was able to run completely.

[mayasheth]

Thanks, I'll mark this as a code issue to resolve permanently in the future.