ctx pyscenic Error

[angelica-varesi]

Hi, I am trying to compute the Cistarget step of pyscenic after obtaining meta cells with the metacell2 pipeline and then the GRN with arboreta package and saved in a tsv file. However, I keep obtaining the same error, which refers to not finding the file or directory even if all the files are present and exist in the specified locations. Could you please help me in fixing this code?

pyscenic ctx /../PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv
/../hg38__refseq-r80__10kb_up_and_down_tss.genes_vs_motifs.rankings.feather /../hg38__refseq-r80__500bp_up_and_100bp_down_tss.genes_vs_motifs.rankings.feather
--annotations_fname /../motifs-v9-nr.hgnc-m0.001-o0.0.tbl
--expression_mtx_fname /../Trial_counts_RNA_metacell_raw_log1p.csv
--output /../Trial_meta_reg.csv
--mask_dropouts
--num_workers 10

: No such file or directory

Thanks a lot to whoever helps! Angelica

2. Error encountered:

   ...

Expected behavior A clear and concise description of what you expected to happen.

Please complete the following information:

• pySCENIC version: [e.g. 0.10.0, use pyscenic -h at the command line]
• Installation method: [e.g. Conda, Pip, Docker, Singularity]
• Run environment: [e.g. Jupyter notebook, CLI, Nextflow, HPC script]
• OS: [e.g. Ubuntu]
• Package versions: [obtain using pip freeze, conda list, or skip this if using Docker/Singularity]:

  ...

[ghuls]

/../PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv is a weird notation for /PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv.

Didn't you mean: ./../PY_SCENIC/TRIAL_PY/Trial_meta_adj.tsv ?