rabies_preprocess.pkl missing

[HelloKitty4lif3]

Hi

I'm trying to run confound correction but receive a "FileNotFoundError: [Errno 2] No such file or directory: 'preprocess_outputs/rabies_preprocess.pkl'" message. Should I have this file after running preprocessing ? I Run this as my preprocessing.

[Gab-D-G]

Hi, yes this file should be there right when you execute the command. Either nothing was executed, or you deleted the file somehow. What gets printed in your terminal?

[colon-perez]

The issue is in the path setting (at least for me). Make sure you set absolute paths (slash before and after the directory, statements below between asterisks), and it should work. Note mine is set for docker, so I mount the directory onto the container, so the absolute path in docker and locally (as you are working) may be different but I hope this helps.

rabies -p MultiProc --local_threads 5 confound_correction **/preprocess_outputs/ /confound_correction_outputs/** ....

[colon-perez]

Thanks, Gabriel, for being so responsive on this discussion board.

[Gab-D-G]

Indeed, absolute paths should always be provided when using Docker/Singularity containers. Thank you for the input @colon-perez . If using a local installation, as seems to be the case with @HelloKitty4lif3 , then it can be fine to use relative paths. Docker can indeed lead to permission issues, if you are still encountering them, consider looking up the examples with --user $(id -u) shown here https://rabies.readthedocs.io/en/latest/running_the_software.html#:~:text=%2D%2Duser%20%24(id%20%2Du)%20can%20be%20added%20to%20mitigate%20writing%20permission%20issues%20when%20using%20Docker.

[colon-perez]

Mine is working now. I mentioned the path because working directories may have been altered as @HelloKitty4lif3 was working on her dataset and now the relative path may wrong. Hopefully they figure it out.

[HelloKitty4lif3]

Thank you for the help @colon-perez and @Gab-D-G. It was a typo of the preprocess path. However, I am met with the same error now but with a missing rabies_preprocess_workflow.pkl now.

Any suggestions where I might have gone wrong?

[Gab-D-G]

This means the preprocessing was not completed. Can you inspect the log for an error?

[gdevenyi]

User is not using the container, they need to reproduce this using the supported release.