Program stalls after 4 hours?

[13thxaro]

Hello,

I am trying to analyze a data set with 6 replicates but for some reason the program seems to stall after 4 hours during the 1000 simulations step. The cpu usage according to docker suddenly drops from 400% to 0.1% and the memory usage drastically drops as well. It has been stuck like this for over 12 hours. Is there a way to work around this? It works fine with 3 replicates but I would like to do all 6 if possible.

[Violet0004]

Hello, I am having the same issue as 13thxaro. I have tried running the docker container. The SURF_count function worked fine for my 3 rep dataset (as well as a 6 rep dataset). However, for both it holds up at the 1000 simulations step (for almost 3 days... you can either call me persistent or stubborn, either works)

My sgRNA list is ~16,000 so I couldn't analyze via the interactive web interface with my dataset in full. However, to test my sgRNA counts file/format output from the SURF_count step, I abridged my list to the 10,000 sgRNA limit for the web site and it ran via that interface just fine (the deconvolution step took 37 minutes... as opposed to the 48 hours that it's been held up on in the Docker container). So it seems the "counts" output is fine.

I also tried cloning the entire repository and running via the command line. That doesn't even make it past the deconvolution step for the first rep.

Are there updated scripts or an updated Docker container available for those of us who can't run our entire dataset on the web site?