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Error running GRNBoost2 step #525
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Did you try with less number of workers? |
Tried with 10 workers, this was the end of the error message:
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How much RAM do your have? You might need to lower the number of threads even more. Also note that we only run pySCENIC on servers and not on local computers (which might not have enough RAM). |
Ah I see I'll try on a server then, thank you |
Hi, I also encountered a problem when running GRNBoost2 step: pyscenic grn --num_workers 20
I am using pySCENIC 0.12.1+2.geaf23eb on a 24 core 1000G RAM HPC
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I met the same problem. I guessed it was probably due to version incompatibility. So I changed the version of packages. However, it didn't work. And when I input as follows, it ran out results. |
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Also the same problem. It seems that this issue has only arisen recently. |
Changing dask/distributed version worked for me. |
If you got error message of "TypeError: Must supply at least one delayed object", You could avoid this message by down-grading dask-expr package, by following code |
git version of arboreto should fix this: aertslab/arboreto#39 |
Merci bcp!!! C'etait Vrai!!! |
Hi guys, I used HPC without Root access. and I use conda environment and command line of pyscenic. |
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Hi @yifanfu01 I don't know if you're still struggling with the installation, but if it's the case I think dask depends on distributed so you have to choose the same version for both of them. |
running into this issue, aertslab/arboreto#33, when trying to install arboreto from source.. |
Error running:
pyscenic grn
--num_workers 20
--output adj.tsv
--method grnboost2
PBMC10k_filtered.loom
hs_hgnc_tfs.txt
Package list:
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