Hanging and NaN output when using covariates.

[mfurla]

Dear developers,

Thank you for your excellent work.

I am running Piranha on a CLIP-seq dataset with IP and IgG in two biological replicates.

I would like to compare four different modalities: IP with and without covariates (bin_size_both = 50, cluster_dist = 100), IP with covariates (cluster_dist = 0), and IgG (without covariates).

For replicate two, I was able to complete all my analyses without issues, but for replicate one I cannot obtain the results with covariates because the software hangs.

I also tried running it on 10% of the dataset (the tail of the BED files), and I obtained a puzzling output:

9 96890150 94493573110080 -nan -nan
9 96890150 33554464 -nan -nan

Could I ask for your feedback?

Thank you,

Mattia