run.neighborhoods.py Dimension Mismatch

[ahelv]

Hi, I am getting an AssertionError: dimension mismatch when running run.neighborhoods.py. The error produced is included below. Any insight as to what is causing the error is appreciated!

thanks, Annika

[thouis]

Hi, could you try this branch and see if it fixes the issue: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/use_pysam

[ahelv]

Hi, I tried running with the branch you posted but the issue persists.

[thouis]

Hi Annika,

Is there some way we could get copies of the data you're trying to run this on?

[ahelv]

Indeed, I first ran into this issue using publicly available data:

DHS: SRX1161152 (replicate 1), and SRX1161153 (replicate 2) H3k27Ac: SRX3083139

I did not have any issue when using the following H3k27Ac data instead H3k27Ac: SRX5806607 (replicate 1) and SRX5806608 (replicate 2)

I have again encountered this same error with some "in house" data.

[thouis]

Great. Which gene annotation file were you using?

[ahelv]

I used RefSeqCurated.170308.bed.CollapsedGeneBounds.bed

[thouis]

Could I ask you to try one more thing before I align these files and try to run:

• Could you make sure the ABC_output directory has been removed (to make sure no files are being cached).
• Could you try the no_promoter_overlaps branch?

[ahelv]

I tried this and I am still getting the same error

[atancoder]

We've revamped the codebase. Please check out https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main and reopen your issue if it still exists