Snakemake failed

[aekendig]

I'm getting the following error when I run the snakemake command:
Error in rule process_data:
jobid: 2
output: input_data/for_model_avgs.csv
shell:

      docker build --tag=data_cleaning -f Dockerfile . 
      docker run -v $(pwd)/:/home/jovyan/project_hydrology data_cleaning
      
    (exited with non-zero exit code)

This error was reproduced by @jiannan0721 and @Yohnjparra

[emchristensen]

It's probably a remnant path issue -- we rearranged the locations of files about 5 times yesterday and may have missed a path change in the read/write to csv commands in a python file...

[aekendig]

We thought that maybe Snakefile_datacleaning was the intended Snakefile because the output matches the output described in the ReadMe. We tried deleting Snakefile and renaming Snakefile_datacleaning and got the following error:

python: can't open file 'prepare_flood_events_table.py': [Errno 2] No such file or directory
[Fri Jul 26 13:54:14 2019]
Error in rule prepare_flood_events:
jobid: 2
output: input_data/flood_events.csv
shell:
python prepare_flood_events_table.py
(exited with non-zero exit code)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

I think this is because prepare_flood_events_table.py is a .ipynb file

[aekendig]

@jiannan0721 figured it out! We just needed to do:
$ cd data_cleaning
before
$ snakemake

[emchristensen]

Sorry there are like 3 snakemake files in that repo. We had bigger plans.