Unable to run cisTarget (pySCENIC)

I ran the GrnBoost2 algorithm on my bulk transcriptomics data and now want to predict regulon using cisTarget. My code raised "could not convert string to float: " error.

ADJACENCIES_FNAME:

	TF	Target	Importance
0	ZFY	DDX3Y	271.644764
1	ZFY	EIF1AY	249.632524
2	ZFY	CYorf15A	249.479488
3	ZFY	USP9Y	242.145026
4	ZFY	KDM5D	215.670768

Run pySCENIC:

!pyscenic ctx {ADJACENCIES_FNAME} {DBS_PARAM} \
            --annotations_fname {MOTIF_ANNOTATIONS_FNAME} \
            --expression_mtx_fname {EXP_MTX_QC_FNAME} \
            --output {MOTIFS_FNAME} \
            --num_workers 26

Traceback:

2022-10-04 13:49:42,020 - pyscenic.cli.pyscenic - INFO - Creating modules.

2022-10-04 13:49:47,486 - pyscenic.cli.pyscenic - ERROR - could not convert string to float:

pyscenic

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written 3.8 years ago by melissachua90 •

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