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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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Tutorial 3 error parse_args_output #78

Closed Torti11 closed 3 months ago

Torti11 commented 11 months ago

Hi,

I tried running tutorial 3 with my Visium data and I got this error. Then, I tried running tutorial 3 with the example data and I got the same error: C:\Users\Downloads\ecotyper-master>"C:\Program Files\R\R-4.3.1\bin\Rscript.exe" C:\Users\Downloads\ecotyper-master\EcoTyper_recovery_visium.R -c C:\Users\Downloads\ecoptyper-master\config_recovery_visium.yml Error in if (grepl("^\{|^\[", output)) { : the condition has length > 1 Calls: -> parse_args_output Execution halted

This error appears independently that the user and token are provided or not in the YAML configuration file. I tried removing the already generated output in VisiumOutput folder and the same error keeps. By the way, I could run the example Bulk data from tutorial 1 without any problems, therefore, EcoTyper is working in my computer but not for Visium data. The previous command was run in the Command Promt of a Windows 11 Pro. Could you help me to figure out the problem, please?

Many thanks in advance!

BALuca commented 10 months ago

Hello,

EcoTyper has not been tested Windows. So, we cannot guarantee that all tutorials work there. Unfortunately, it is hard to debug the problem from the message above. Causes can include a Windows-specific error, a problem with the configuration file, or a bug in the code. Would it be possible to run it on a Linux/Mac machine? If the error persists, could you please send us the configuration file you used at ecotyper.stanford@gmail.com?

Best regards, The EcoTyper team