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

[iammrtza]

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?