Changed status from running to waiting

[naiarabediaga]

Hi There,

I am trying to run the example command cmd.sh, but it gets stuck and shows the message "Changed status from running to waiting" and it can go like this for hours. Any idea what it might be happening?

[driestk]

Hi,

Have you previously run the example command cmd.sh or run the pipeline to the same output directory? The pypiper pipeline will generate lock files if interrupted to prevent overwriting files while the pipeline is running, but these will also cause the pipeline to get "stuck" and give the message "Changed status from running to waiting".

To fix this you can either: Delete the lock files (rm lock*) in the output directory or Run the example command with the -R or --recover flag to overwrite lock files

More details on using pypiper can be found here: https://pypiper.readthedocs.io/en/latest/usage.html

[naiarabediaga]

Thank you so much! It perfectly works now.

Best

Naiara

El jue., 11 abr. 2019 a las 11:00, driestk (notifications@github.com) escribió:

Hi,

Have you previously run the example command cmd.sh or run the pipeline to the same output directory? The pypiper pipeline will generate lock files if interrupted to prevent overwriting files while the pipeline is running, but these will also cause the pipeline to get "stuck" and give the message "Changed status from running to waiting".

To fix this you can either: Delete the lock files (rm lock*) in the output directory or Run the example command with the -R or --recover flag to overwrite lock files

More details on using pypiper can be found here: https://pypiper.readthedocs.io/en/latest/usage.html

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-- Naiara Garcia Bediaga, PhD