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ay-lab / FitHiChIP

Statistically Significant loops from HiChIP data
MIT License
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Halts at Regression Model #70

Closed vivianschu closed 2 years ago

vivianschu commented 2 years ago

Hi, when running FitHiChIP, all scripts halt at the same line at the Regression model but does not crash (simply runs until there is no time left):

 === Regression model (training data) - average distance: 165000 number of interactions: 45444  number of bias threshold satisfying interactions: 42380

 === Regression model (training data) - average distance: 170000 number of interactions: 44950  number of bias threshold satisfying interactions: 41784

 === Regression model (training data) - average distance: 175000 number of interactions: 44457  number of bias threshold satisfying interactions: 41375
~

I am using 10 CPUs and 50 gb of memory. This is being run on GRCh38. Do you have any ideas to why this is happening? Thanks!

vivianschu commented 2 years ago

I've downloaded the latest version of FitHiChIP and it seems to be halting at the same step for regression (does not fail, just keeps running):

 ****** Start regression - Equal Occupancy binning ****

Would you be able to help? Thanks!

ay-lab commented 2 years ago

Hi @vivianschu Thanks for your query. Could you please e-mail me (sourya@lji.org) the following? 1) output log file 2) The file "Bin_Info.log" within the same output directory containing FitHiChIP significant interactions I'll check the output and get back to you soon.

ay-lab commented 2 years ago

Hi @vivianschu Are you still having the issue?

ay-lab commented 2 years ago

Hi @vivianschu Could you please "git clone" the current code and test it on your data? I've updated the parallel processing routine. Let me know if it solves your problem.

vivianschu commented 2 years ago

Hi @ay-lab, thanks for your help - everything works great now.