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aertslab / SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
GNU General Public License v3.0
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How long for pyscenic ctx to run? #75

Open igrisch opened 12 months ago

igrisch commented 12 months ago

Hello,

I'm currently running the Docker version of pyscenic (0.12.1) on HPC (Fedora). All was OK until I hit the pyscenic ctx command. My command is below:

pyscenic ctx \ ./expr_mat.adjacencies.tsv \ software/SCENIC/resources/databases/new/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather \ software/SCENIC/resources/databases/new/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather \ --annotations_fname software/SCENIC/resources/motif2tf/motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl \ --expression_mtx_fname ./expr_mat_filtered.tsv \ --mode "custom_multiprocessing" \ --output ./regulons_mask_dropouts.csv \ --mask_dropouts So far, I've tried running it multiple times and it always goes quickly until the "pyscenic.prune" step where I will get the following messages and then it freezes indefinitely (so far we are at 2 days for one of my attempts):

`2023-07-18 16:01:10,759 - pyscenic.prune - INFO - Worker hg38refseq-r8010kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings(14): All regulons derived.

2023-07-18 16:01:10,759 - pyscenic.prune - INFO - Worker hg38refseq-r8010kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings(14): All regulons derived.

2023-07-18 16:01:11,050 - pyscenic.prune - INFO - Worker hg38refseq-r8010kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings(14): Done.

2023-07-18 16:01:11,050 - pyscenic.prune - INFO - Worker hg38refseq-r8010kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings(14): Done. ` I get these messages for presumably all 32 workers? It will give this message for numbers 1-16.

What can I do to get past this infinitely-running part of pyscenic ctx? Or does it just take a long time? For context, I have about 7k cells, but I'm using a SMART-seq-based method, so more genes than 10x.

LacquerHed commented 7 months ago

Ever figure out why is freezes at this step?

arunchakra commented 1 month ago

dealing with the same thing. Anybody solve this issue?