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Reed-CompBio / spras

Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
MIT License
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Cytoscape workflow error on 1000 runs #171

Open D3xtersLab opened 3 months ago

D3xtersLab commented 3 months ago

I ran Omics Integrator with a Beta parameter set to 1000 values between 1 and 2. All other parameters were fixed. This caused snakemake to error out and fail to produce a cytoscape file. I tried this with 500, 375, and 250 values. 250 worked but the rest still failed.

Cyto_Error
agitter commented 2 months ago

The Java heap space is defined in the Cytoscape.vmoptions file in the Docker image. We could modify this when we build the Docker image to support larger pathways and more pathways. It would be hard to dynamically allocate more heap space based on the number of pathways to load.