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IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
https://umgear.org
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Dr #464

Open gear-portal-team opened 1 year ago

gear-portal-team commented 1 year ago

From: Gavin Clowry

Email: gavin.clowry@ncl.ac.uk

Server IP: 10.142.0.14

Msg: We have been happily generating UMAP plots form a particular data set, human thalamus 18 GW, but now, when we get to the Louvain clustering step, we get an error message. Have we forgotten something or is there a bug in the system? I have tried to attach a screenshot but can't get that to work either.

Tags: ['Louvain']

Screenshot: None

adkinsrs commented 1 year ago

I dealt with a recent issue like this on my local computer. The issue was that the louvain clustering step runs out of memory and just exits with a failure with no error message. The way I solved this was by changing the "flavor" option from sc.tl.louvain from "vtraag" to "igraph" which consumes less memory. However, this was for testing purposes, and since this option affects the clustering algorithm, it would probably have an effect on the louvain output. So I am hesitant to recommend fixing in this manner.

adkinsrs commented 1 year ago

Also, there was a permissions issue on the NeMO server for uploading screenshots. I fixed that

adkinsrs commented 1 year ago

Addressing the screenshot upload side-issue in #465