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nextflow pipeline error: Signatures dataframe is empty
Hi there! I tried the nextflow tool for running scenic. The command error happened in the following code :
2022-05-17 00:43:43,002 - pyscenic.cli.pyscenic - INFO - Loading gene signatures.
Traceback (most recent call last):
File "/opt/venv/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/opt/venv/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 470, in main
args.func(args)
File "/opt/venv/lib/python3.7/site-packages/pyscenic/cli/pyscenic.py", line 220, in aucell_command
signatures = load_signatures(args.signatures_fname.name)
File "/opt/venv/lib/python3.7/site-packages/pyscenic/cli/utils.py", line 175, in load_signatures
return df2regulons(load_motifs(fname, sep=suffixes_to_separator(extension)))
File "/opt/venv/lib/python3.7/site-packages/pyscenic/transform.py", line 308, in df2regulons
assert not df.empty, 'Signatures dataframe is empty!
AssertionError: Signatures dataframe is empty!`
I checked the config and thought it may be associated with the threshold in the config:
cistarget {
adj = 'adj.tsv'
type = ''
rank_threshold = 5000
auc_threshold = 0.05
nes_threshold = 3.0
min_orthologous_identity = 0.0
max_similarity_fdr = 0.001
annotations_fname = ''
thresholds = '0.75,0.90'
top_n_targets = 50
top_n_regulators = '5,10,50'
min_genes = 20
all_modules = false
motifsDb = 'pyscenic/mm10/mm10__refseq-r80__*feather'
motifsAnnotation = 'pyscenic/mm10/motifs-v9-nr.mgi-m0.001-o0.0.tbl'
}
which threshold should I change? Will it result in different regulons? Can anyone help me?