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kundajelab / chrombpnet

Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
https://github.com/kundajelab/chrombpnet/wiki
MIT License
115 stars 32 forks source link

chrombpnet prep nonpeaks does not complete #210

Open Brawni opened 4 hours ago

Brawni commented 4 hours ago

Dear devs,

I'm stuck at trying to generate non-peak regions using function chrombpnet prep nonpeaks as the progress bar freezes at 22% with my current peakset. I tested this on tutorial and the function successfully complete and also on a subset of the peaksets i input sampling 200,000 peaks out of the ~800,000 peaks i'm using. I tried to run it with more memory / cores but it doest change and it always stops at 22%.

Any input would be much appreciated!

Thank you!!

akundaje commented 4 hours ago

800,000 is way too many peaks. Restrict to the top 250K peaks

On Wed, Oct 9, 2024 at 12:04 PM Bruno Giotti @.***> wrote:

Dear devs,

I'm stuck at trying to generate non-peak regions using function chrombpnet prep nonpeaks as the progress bar freezes at 22% with my current peakset. I tested this on tutorial and the function successfully complete and also on a subset of the peaksets i input sampling 200,000 peaks out of the ~800,000 peaks i'm using. I tried to run it with more memory / cores but it doest change and it always stops at 22%.

Any input would be much appreciated!

Thank you!!

— Reply to this email directly, view it on GitHub https://github.com/kundajelab/chrombpnet/issues/210, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABDWEI3I5RTIAEUPI5UXQDZ2V44PAVCNFSM6AAAAABPVGBE5KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3TMNZSGQ3TMMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Brawni commented 4 hours ago

Will do thanks!