galaxyproject / galaxyproject/training-material
Jupyter notebook (JupyLab tool) resources limit?
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Description
I’m doing an analysis using salmon alevin command and after running the command the process stops at around 25% of analysed cells (that’s around 6500 cells - I know that from the output log). It happens when I’m doing it in jupyter notebook (JupyLab tool) but the notebook cell has [*] next to it suggesting that it’s still running (but no new log output is displayed). But when I run the same command with the same input files locally (VSC) the analysis goes to completion.
I had to massively down sample the dataset for that command to be executed successfully on .eu server. Interestingly, the same dataset still fails on .org server.
I have no idea what causes that - is there a resource limit on interactive jupyter notebook? Well, I used monocle3 and did huge dimensionality reduction in jupyter notebook which seemed to be much more computationally intensive and took up to 15mins - but it worked, in contrast to alevin now...
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