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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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issue running GENIE3 on calculation cluster and scenic on computer #126

Closed vbouther closed 2 years ago

vbouther commented 4 years ago

Hello scenic community, I am trying to run scenic on a 900*4500 matrix. I had to run genie3 on a cluster as my computer was not powerful enough but I was hoping to run the rest of the code on my computer, as it is very challenging to install packages on the cluster. I've downloaded the weight matrix generated by GENIE3 on the cluster as a RData file and reload it on my rstudio session, it worked fine. However, when I attempt to run the very first step of SCENIC, here is the error message: runSCENIC_1_coexNetwork2modules(scenic_opts) Error in .local(object, ...) : File 'int/1.4_GENIE3_linkList.Rds' does not exist.

I have reloaded the scenic_opts file but didnt work any better. In my int folder I only have: ls int 1.1_genesKept.Rds 1.2_corrMat.Rds scenic_opts.Rds

I feel like there are some files that have been created while running GENIE3 on the cluster that are needed to run scenic and I don't know which one and how to get them (I cannot find any int folder on the server).

Has anyone encountered this issue before? Thank you very much!!

EAC-T commented 3 years ago

I'm having the same problem, I didn't use a cluster, I only used my laptop. Have you find out what the issue was? I hope you can help. Thank you