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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Expression matrix should be provided in the loom file format.[BUG] #553

Open bitcometz opened 1 month ago

bitcometz commented 1 month ago

hello,

Describe the bug My shell:

pyscenic aucell \
    scenic.loom \
    reg.csv \
    --output pyscenic_output.loom \
    --num_workers 5

My log

2024-06-13 13:14:58,995 - pyscenic.cli.pyscenic - INFO - Loading expression matrix.

2024-06-13 13:15:01,551 - pyscenic.cli.pyscenic - INFO - Loading gene signatures.
Create regulons from a dataframe of enriched features.
Additional columns saved: []

2024-06-13 13:15:04,886 - pyscenic.cli.pyscenic - INFO - Calculating cellular enrichment.

2024-06-13 13:15:44,567 - pyscenic.cli.pyscenic - INFO - Writing results to file.

2024-06-13 13:18:18,668 - pyscenic.cli.pyscenic - ERROR - Expression matrix should be provided in the loom file format.

Based on the log of my execution results, it appears that I have run successfully. Why am I still getting error messages :

ERROR - Expression matrix should be provided in the loom file format.

Could you please help with this? Thanks !!!

wangtanzhang612 commented 1 month ago

same issue

RickyMaGZ commented 1 month ago

I came across with exactly same issue. Did you find any solution for it?