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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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scenicplus prepare_data prepare_menr error #470

Open Yiming-Huang-neuron opened 2 months ago

Yiming-Huang-neuron commented 2 months ago

HI, Can you help me how to solve the problems with the "scenic plus prepare_data prepare_menr?"

I try each step to run the code. I try the pipeline in mouse species. I'm getting the following error, here is my code.

code

Yiming-Huang-neuron commented 2 months ago

code3

Yiming-Huang-neuron commented 2 months ago

Here is my error error I have found someone who have the same mistakes，but i have checked the error which do not happen in my data.

Please help me.

All the best

Yiming

SeppeDeWinter commented 1 month ago

Hi @Yiming-Huang-neuron

One or more of your cistromes seems to be empty ... Can you check wether this is the case?

All the best,

Seppe

Yiming-Huang-neuron commented 1 month ago

Hi, @SeppeDeWinter thank you for your reply.

As you say, I have checked the ctx_results.hdf5 and dem_results.hdf5. They both "cistromes/region_set" and "cistromes/database" are empty.

I try to run "scenicplus prepare_data prepare_menr" and "scenicplus grn_inference motif_enrichment_dem" again.

This is my error file

微信图片_20241011170658

There are only warnings and no errors. It looks like out of memory. I have four species, each with 100k cells. I have successfully run the human dataset, but the remaining three species generate this warning. Then I reran the human data and got the same warning with no data.

Is there any way to avoid memory errors and generate files normally?

All the best

Yiming

yojetsharma commented 1 month ago

Hi, @SeppeDeWinter thank you for your reply.

As you say, I have checked the ctx_results.hdf5 and dem_results.hdf5. They both "cistromes/region_set" and "cistromes/database" are empty.

I try to run "scenicplus prepare_data prepare_menr" and "scenicplus grn_inference motif_enrichment_dem" again.

This is my error file 微信图片_20241011170658

There are only warnings and no errors. It looks like out of memory. I have four species, each with 100k cells. I have successfully run the human dataset, but the remaining three species generate this warning. Then I reran the human data and got the same warning with no data.

Is there any way to avoid memory errors and generate files normally?

All the best

Yiming

You could try running it manually as they have pointed out in other issues. But what helped my case with memory errors was reducing the cores for the job.

SeppeDeWinter commented 1 week ago

@Yiming-Huang-neuron

Could you share the entire stack trace + command you were running so we can help troubleshooting further?

All the best,

Seppe