Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

pyscenic ctx Error: pandas.errors.ParserError: Could not construct index. Requested to use 2 number of columns, but 3 left to parse #512

Open
zhrmxxs opened this issue Nov 19, 2023 · 2 comments
Labels
bug Something isn't working

Comments

@zhrmxxs
Copy link

zhrmxxs commented Nov 19, 2023

Hello pyscenic team,
I am experiencing an error while running pyscenic ctx: 'pandas.errors.ParserError: Could not construct index. Requested to use 2 number of columns, but 3 left to parse.'
The code I run is as follows:
pyscenic ctx \ test_adj.sample.tsv \ maize.regions_vs_motifs.rankings.feather \ --annotations_fname maize.tbl \ --expression_mtx_fname test.loom \ --mode "dask_multiprocessing" \ --output test_regulon.csv \ --num_workers 3 \ --mask_dropouts

I have checked the corresponding input file and can't find any errors.

@zhrmxxs zhrmxxs added the bug Something isn't working label Nov 19, 2023
@zhrmxxs zhrmxxs closed this as completed Nov 19, 2023
@zhrmxxs zhrmxxs reopened this Nov 19, 2023
@zhrmxxs
Copy link
Author

zhrmxxs commented Nov 19, 2023

'pandas.errors.ParserError: Could not construct index. Requested to use 2 number of columns, but 3 left to parse' is the middle error and the final error is 'pyscenic.cli.pyscenic - ERROR - No columns to parse from file'

@ghuls
Copy link
Member

ghuls commented Dec 12, 2023

Very likely, one of your input files is not formatted properly at a certain line.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

2 participants