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digitalcytometry / ecotyper

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
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cp: Cannot stat #71

Closed dmiyagi closed 1 year ago

dmiyagi commented 1 year ago

Hi sorry this should be my last post! love your tools.

I ran Cytospace to get cell fractions. I keep getting this error even though I'm 1000% sure the file is where it is supposed to be and that there are no extra spaces in the path as it seems to show between the quotes. any suggestions? I'm so close!


Loading user-provided cell type fractions...
cp: cannot stat ' /gpfs/gibbs/project/path/to/tools/Ecotyper/ecotyper/Y0848_fractional_abundances_by_spot.txt ': No such file or directory
Error in RunJobQueue() : 
  EcoTyper failed. Please check the error message above!
Execution halted
dmiyagi commented 1 year ago

Hi,

I wanted to update you that I tried with the carcinoma data on my spatial data and am still getting that cp stat error that it can't see the file even though (in the same notebook) I am able to reproduce the file you have in your tutorial. Something is amiss. Would appreciate any suggestions!

Screenshot 2023-07-17 at 11 08 50 AM

Screenshot 2023-07-17 at 11 09 23 AM Screenshot ![Screenshot 2023-07-17 at 11 09 23 AM](https://github.com/digitalcytometry/ecotyper/assets/47726144/da8335a4-5909-49ee-ab61-e3590a6c6145) 2023-07-17 at 11 08 45 AM

BALuca commented 1 year ago

Dear Danielle,

Thank you for your interest in EcoTyper. Apologize for the issue you are encountering with recovery in Visium data. It seems that there was, indeed, a small bug introduced at the previous commit. I fixed it and the latest version of EcoTyper from GitHub should solve your problem. Please let us know if you are still getting errors.

Best regards