Describe the bug
I was previously using pyscenic to identify regulons in my scRNA-Seq data. To ensure robustness of the regulons identified, I used VSN scenic with multiruns. I tried running the example given in the documentation and it works for nRuns = 2. However, when I used my own dataset and increase nRuns = 100, it stalls (once at 21%, and another at 64%) during the Arboreto with multiprocessing step. The CPU usage percentage drops to 0% so it doesn't seem to be running, even though there is no error shown. I apologise that I could not include the screenshot as I tried to restart the process with -resume, but now it seems to have skipped the Arboreto step with 64% to the next step (add Pearson correlation). I was wondering if this had to do with the config file compute resources, so I increased some of the parameters. I am quite new to this so I am not sure which exact parameter to toggle, so could you kindly take a look at my config file? I am running it on a local workstation, with 16 cores/32 threads, with 120GB RAM.
I have attached the config file and execution trace in .txt files, and the reports and timeline in pdf files. The 65th run for arboreto stalled for 5 hours+ before I Ctl+C to force stop. I would appreciate some guidance on the compute resource parameters - specifically, does the cpus in the config refer to number of cores or threads as well?
Describe the bug I was previously using pyscenic to identify regulons in my scRNA-Seq data. To ensure robustness of the regulons identified, I used VSN scenic with multiruns. I tried running the example given in the documentation and it works for nRuns = 2. However, when I used my own dataset and increase nRuns = 100, it stalls (once at 21%, and another at 64%) during the Arboreto with multiprocessing step. The CPU usage percentage drops to 0% so it doesn't seem to be running, even though there is no error shown. I apologise that I could not include the screenshot as I tried to restart the process with -resume, but now it seems to have skipped the Arboreto step with 64% to the next step (add Pearson correlation). I was wondering if this had to do with the config file compute resources, so I increased some of the parameters. I am quite new to this so I am not sure which exact parameter to toggle, so could you kindly take a look at my config file? I am running it on a local workstation, with 16 cores/32 threads, with 120GB RAM.
To Reproduce Steps to reproduce the behavior:
Configure with these options:
Run using this entry point:
See error: Stalls at a certain percentage, with 0% CPU usage. I have to Ctl+C to force stop.
Expected behavior Process should continue.
Please complete the following information:
Additional context config.txt execution_trace.txt [angry_roentgen] Nextflow Workflow Report.pdf execution_timeline.pdf
I have attached the config file and execution trace in .txt files, and the reports and timeline in pdf files. The 65th run for arboreto stalled for 5 hours+ before I Ctl+C to force stop. I would appreciate some guidance on the compute resource parameters - specifically, does the cpus in the config refer to number of cores or threads as well?
Thank you so much!