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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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[BUG] empty adjacencies file when running pyscenic grn via docker #563

Open iammrtza opened 3 months ago

iammrtza commented 3 months ago

Describe the bug I am running the grn part of the pyscenic through docker as exactly shared here ("https://pyscenic.readthedocs.io/en/latest/installation.html#command-line-interface"). The code runs without error but I get empty adjacencies.tsv file.

My input data frame is a count matrix with cells as rows and genes as columns. Ialso input the TF file.

below is my code: 

EXPRESSION_MATRIX="/data/df.tsv"
TF_LIST="/data/mm_tfs.txt"
ADJACENCIES="/data/adjacencies.tsv"
MODULES="/data/regulons.tsv"
AU_CELL_RESULTS="/data/aucell_results.tsv"
MOTIF_ANNOTATIONS="/data/motifs-v9-nr.mgi-m0.001-o0.0.tbl"

RANKINGS="/data/mm9-tss-centered-5kb-10species.mc9nr.genes_vs_motifs.rankings.feather \
         /data/mm9-tss-centered-10kb-10species.mc9nr.genes_vs_motifs.rankings.feather"

docker run -it --rm -v /data:/data aertslab/pyscenic:0.12.1 pyscenic grn --num_workers 6 -o $ADJACENCIES $EXPRESSION_MATRIX $TF_LIST

What is the problem?

ghuls commented 2 months ago

Does the /data directory contain the mentioned files?