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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Can you restart the pipeline from a given step? #263

Closed mason-sweat1 closed 7 months ago

mason-sweat1 commented 7 months ago

Thanks for the cool package, I am excitedly processing my data and can't wait to see the results.

I am on the final step, using the wrapper to create scienic plus obj.

However, I keep having things go wrong. For example, I had the low memory error due to Numba incompatability.

Is there a way to re-start the pipeline from a particular step? For example, if it crashed on make UMAP, could i just start from that step and work down? Each try takes almost 24 hours due to the number of cells I am integrating, so this would be helpful.

Thanks, Mason

SeppeDeWinter commented 7 months ago

Hi @mason-sweat1

The results of each step should be saved in your scplus_obj. So as long as you still have access to that object (i.e. you saved it to your hard drive), you can recover the progress that has been already made without the need of rerunning the entire pipeline.

In fact, all necessary steps have already been completed if you manage to reach the UMAP generation step.

All the best,

Seppe

mason-sweat1 commented 7 months ago

Dear Seppe,

I see that now, thank you very much!

I will close this out but had one other question.

Edit: I asked an uninformed question but quickly found the answer. Thanks.

Mason

SeppeDeWinter commented 7 months ago

Hi @mason-sweat1

Happy to help.

No worries!.

All the best,

Seppe