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tanaylab / metacells

Metacells - Single-cell RNA Sequencing Analysis
MIT License
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ctx pyscenic Error #71

Closed angelica-varesi closed 2 months ago

angelica-varesi commented 2 months ago

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 \ /../hg38refseq-r8010kb_up_and_down_tss.genes_vs_motifs.rankings.feather /../hg38refseq-r80500bp_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

orenbenkiki commented 2 months ago

It probably has nothing to do with MC2. Off the top of my head, the path of the files seems wrong; /../whatever is an absolute path saying "go to the root of the file system, then go one level up, then go down to whatever. This path makes no sense since there's nothing "above" the root of the file system.