Open Chromatin Predict Stuck

[zhihao6201]

Thanks for developing this useful tool.

I am having trouble on Open Chromatin Predict(modkit open-chromatin predict). The output always stop writing at some point and I receive no error message. It just gets stuck for a very long period of time. I am using a bam file(about 3GB) with low coverage so I set the threshold --min-coverage 2 for my commands. I saw similar issue in the github so I also add the super-batch-size and batch-size as they suggested. However, it is till not working.

Below is the command I used: nohup modkit open-chromatin predict --model [email protected] --output ../output/barcode03_cov2.bedGraph --device 0 --min-coverage 2 --super-batch-size 10 --batch-size 64 ../input/barcode03.sorted.bam > barcode03_cov2.log 2>&1 &

I have tried removing the min-coverage 2 and it seems that it can finish. I am wondering whether it is because I set the coverage threshold too low? Also, if I really need to set this low coverage, how could I solve this stuck issue?

[ArtRand]

Hello @zhihao6201,

Sorry about this, there is a bug where if Modkit cannot get enough GPU memory it can stall. I'm working on a fix. In the mean time there is a workaround to get the program to run, if you add --super-batch-size 10 --batch-size 64 to your command it should progress. If it doesn't let me know.