[BUG]Running grn but discontinued without any errors

[LynnChan99]

Hi, thank you for this wonderful package. I have two questions for its application.

(1) I run the whole process without any errors in my python, only many warnings like 'less than 80% of the genes in xxx could be mapped', and I could only get a few TFs (less than 10) in my output files. But other example data seems to have much more TFs in their results. I still can't figure it out why.

(2) Then I tried to use this tool in docker desktop. However, I run the code following your tutorial, but it would be disrupted suddenly without any error or warning, the output line only have this normal message.

(base) chan@MacBook-Air ~ % docker run -it --rm \
--platform linux/amd64
-v $HOME/Desktop/data:/data
aertslab/pyscenic:0.12.1 pyscenic grn
--num_workers 6
-o /data/NK.T.grn.tsv
--transpose \
/data/NK.T.loom \
/data/allTFs_hg38.txt
2025-08-12 02:59:44,784 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

Looking forward to your reply, thank you so much.

[LynnChan99]

For question1, no pruning or adjust defualt parameters of max_similarity_fdr, rank_thereshold, etc. in the second step(ctx) might be helpful to produce more TFs.

[LynnChan99]

For question2, might be memory problems? but it could run smoothly in my terminal.