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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Missing Expected Outputs in SCENIC+ Pipeline #486

Closed yojetsharma closed 3 weeks ago

yojetsharma commented 1 month ago

I am currently using the SCENIC+ pipeline, and I've encountered an issue where several expected outputs are missing from the results. Specifically, the following outputs are not being generated: AUCell_direct: 0 AUCell_extended: 0 eGRN_extended: 0 scplus_mudata: 0

Expected Behavior: I expect the pipeline to generate these outputs as part of its normal operation. Current Behavior: The pipeline runs successfully and returns a limited number of outputs, with no error messages in the log file. The job count indicates only one for AUCell_direct, AUCell_extended, eGRN_extended, and scplus_mudata, which is not the expected outcome. Environment: SCENIC+ version: 1.0a1 Python version: 3.11

Edit: going through some other older issues makes it a memory issue. So I checked how much was being allotted and used up. If this is a memory issue then: I had asked for vmem of 250, it requested for 170GiB more so I upped vmem to 500G still the same error. The cores were reduced to 5-10. Didn’t help either. The imputed obj generated in the pycistopic pipeline was around 184GiB and still all of it ran smoothly as job but not sure about AUcell.

Any idea/suggestions how to go about this?

yojetsharma commented 1 month ago

Running it with the vmem 150G and 1 core, solved the issue and generated all the expected outcomes.