IndexError: list index out of range for path_raw = all_path[0]

[wasimsandhu]

I'm getting what I hope is just a usage error when I try to use SLAW with some of my data. They are Thermo Q-Exactive RAW files that were converted to mzML using MSConvert. Data files are stored in SLAW_Test\input and parameters text file is stored in SLAW_Test\output.

I used the parameters.txt from the test_files Github directory, but when running the above line of code without a parameters file, no parameters file is generated in SLAW_Test\output.

Here is the line of code I'm running in Windows Powershell: C:\Users\eliaslab\Downloads\SLAW_Test>docker run --rm -v input:/input -v output:/output zambonilab/slaw:latest

And here is the error I'm getting:

Traceback (most recent call last):

File "/wrapper_docker.py", line 120, in <module> pol = exp.guess_polarity(INPUT)

File "/pylcmsprocessing/model/experiment.py", line 109, in guess_polarity path_raw = all_path[0]

IndexError: list index out of range

[htmonkey]

Your local folder is specified wrongly. Your volumes should be something like "-v [WINDOWS_PATH]:/input -v [WINDOWS_PATH]:/output'.

[wasimsandhu]

Ah you're right. I assumed starting in the directory would work, I did not know I would have to specify the full path. The following worked for me:

docker run --rm -v C:/Users/eliaslab/Downloads/SLAW_Test/input:/input -v C:/Users/eliaslab/Downloads/SLAW_Test:/output zambonilab/slaw:latest