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This run ended up creating an empty (zero byte) output file shown here:
$ la | grep WT_all_reg.csv
-rw-rw----. 1 username xxxx 0 Feb 9 15:47 WT_all_reg.csv
I'm assuming that my issue is unrelated to unmatched gene symbols across the input files as I found that over 1000 gene symbols intersected across the ranking (.feather), adjacency (adj.csv), TFs (allTFs_mm.txt), and motif (.tbl) files.
# Load ranking databasesfeather=f_db_names['raw'][0]
feather=pd.read_feather(feather)
# Unique gene symbolsfeather_g=list(set(list(feather.columns))) # from feather filetfs_g=list(pd.read_csv(tfs, header=None).iloc[:,0]) # from TF listadj_g=list(set(pd.read_csv(adj_csv).loc[:, 'target'].to_list())) # from adjacencyanno_g=list(set(pd.read_csv(f_motif_path, sep="\t").loc[:,'gene_name']))
# All gene symbols (w duplicates)all_g=tfs_g+adj_g+feather_g+anno_g# Retrieve gene symbols intersecting across the feather, tfs, adj, and tbl filescount=pd.Series(all_g).value_counts().to_dict()
# Save gene symbols found in every file to a listg4= []
forkey, valueincount.items():
ifvalue==4:
g4.append(key)
# >>> len(tfs_g)# 1860# >>> len(adj_g)# 20746# >>> len(feather_g)# 24069# >>> len(anno_g)# 1412# >>> g4[:6]# ['Cpeb1', 'Pml', 'Rcor1', 'Rad21', 'Ascc1', 'Prox1']# >>> len(g4)# 1054assertlen(g4) >0, "Ensure to have gene symbols matched across all input files."
Some testings done so far:
skipping --no_pruning parameter
skipping --mask_dropouts parameter
using v9 ranking files for mm10 (mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather, mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.genes_vs_motifs.rankings.feather) and/or v9 motif file (motifs-v9-nr.mgi-m0.001-o0.0.tbl)
v9 ranking file + v10 motif file
v10 ranking file + v9 motif file
v9 ranking file + v9 motif file
I saw a few issue reports on empty output but at least they got Writing an output file message.
My environment was HPC being summarized here:
OS
LSB Version: :core-4.1-amd64:core-4.1-noarch
Distributor ID: RedHatEnterprise
Description: Red Hat Enterprise Linux release 8.9 (Ootpa)
Release: 8.9
Codename: Ootpa
I think my CLI code is relatively straightforward. I've been also trying with R and python but none of them are successful. I would like to get some hints or suggestions. Thank you very much for your time!
The text was updated successfully, but these errors were encountered:
I've been seeing my
pyscenic ctx
gets terminated in the middle of the run. My mystery is that it doesn't throw any error message as shown below:It comes back to my terminal without the
Writing an output file
message, which I'm expecting to see if it was successful.My script is following:
$ cat pyscenic_23.sh #!/bin/bash pyscenic ctx \ scrnaseq-pyscenic-tac1-chat/WT_all_adj.csv \ cistarget-db/mm10_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather \ cistarget-db/mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather \ --annotations_fname cistarget-db/motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl \ --expression_mtx_fname scrnaseq-pyscenic-tac1-chat/WT_all.loom \ -o scrnaseq-pyscenic-tac1-chat/WT_all_reg.csv \ --mask_dropouts \ --num_workers 32 \
This run ended up creating an empty (zero byte) output file shown here:
$ la | grep WT_all_reg.csv -rw-rw----. 1 username xxxx 0 Feb 9 15:47 WT_all_reg.csv
I'm assuming that my issue is unrelated to unmatched gene symbols across the input files as I found that over 1000 gene symbols intersected across the ranking (
.feather
), adjacency (adj.csv
), TFs (allTFs_mm.txt
), and motif (.tbl
) files.Some testings done so far:
--no_pruning
parameter--mask_dropouts
parametermm10__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather
,mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.genes_vs_motifs.rankings.feather
) and/or v9 motif file (motifs-v9-nr.mgi-m0.001-o0.0.tbl
)I saw a few issue reports on empty output but at least they got
Writing an output file
message.My environment was HPC being summarized here:
Singularity> pyscenic -h usage: pyscenic [-h] {grn,add_cor,ctx,aucell} ... Single-Cell rEgulatory Network Inference and Clustering (0.12.1+0.gce41b61.dirty)
singularity build aertslab-pyscenic-0.12.1.sif docker://aertslab/pyscenic:0.12.1
singularity-ce version 4.0.1
I think my CLI code is relatively straightforward. I've been also trying with R and python but none of them are successful. I would like to get some hints or suggestions. Thank you very much for your time!
The text was updated successfully, but these errors were encountered: