Error DiaMetAlyzer Python Source node

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1

strong textHello all,

when I try to test the DiaMetAlyzer (latest version (openms 2.7.0, Sirius 4.9.0, …), I get an error message in the “python source” node:

Python Source Error:

C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW*.osw
[‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma3SWATH20-50.osw’]
[‘C:\Users\Adrianbrun\anaconda3\envs\py39\Scripts/pyprophet’, ‘merge’, ‘–template’, ‘/C:/Users/Adrianbrun/AppData/Local/Temp/knime_DIAMetAlyzer%20_249474/fs-Assay_0-375-49486/000/000/AssayGeneratorMetabo_0/sirius.pqp’, ‘–out’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\merged_osw.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step10Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step1Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step2Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step3Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step4Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step5Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step6Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step7Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step8Plasma3SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma1SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma2SWATH20-50.osw’, ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\PestMix1_8Step9Plasma3SWATH20-50.osw’]
merging
Calling pre scored osws merge function
Traceback (most recent call last):
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\runpy.py”, line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\runpy.py”, line 87, in run_code
exec(code, run_globals)
File "C:\Users\Adrianbrun\anaconda3\envs\py39\Scripts\pyprophet.exe_main.py", line 7, in
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\click\core.py”, line 1130, in call
return self.main(*args, **kwargs)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\click\core.py”, line 1055, in main
rv = self.invoke(ctx)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\click\core.py”, line 1688, in invoke
rv.append(sub_ctx.command.invoke(sub_ctx))
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\click\core.py”, line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\click\core.py”, line 760, in invoke
return __callback(*args, **kwargs)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\pyprophet\main.py”, line 273, in merge
merge_osw(infiles, outfile, templatefile, same_run, merged_post_scored_runs)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\pyprophet\levels_contexts.py”, line 555, in merge_osw
merge_osws(infiles, outfile, templatefile, same_run)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\site-packages\pyprophet\levels_contexts.py”, line 560, in merge_osws
copyfile(templatefile, outfile)
File “C:\Users\Adrianbrun\anaconda3\envs\py39\lib\shutil.py”, line 264, in copyfile
with open(src, ‘rb’) as fsrc:
OSError: [Errno 22] Invalid argument: ‘/C:/Users/Adrianbrun/AppData/Local/Temp/knime_DIAMetAlyzer%20_249474/fs-Assay_0-375-49486/000/000/AssayGeneratorMetabo_0/sirius.pqp’
scoring
Usage: pyprophet score [OPTIONS]
Try ‘pyprophet score --help’ for help.
Error: Invalid value for ‘–in’: Path ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\merged_osw.osw’ does not exist.
exporting
Usage: pyprophet export-compound [OPTIONS]
Try ‘pyprophet export-compound --help’ for help.
Error: Invalid value for ‘–in’: Path ‘C:\Volumes\DiaMetAlyzer\Output Folder Quantification\OSW\scored_ms1ms2.osw’ does not exist.

Knime Console Error:
WARN Python Source 0:344:342 Node created an empty data table.

Can someone help me fix this error?
Many thanks in advance!

Best regards,

Adrian Brun

2

@AdrianBrun welcome to the KNIME forum. Could you give us an example of the code or workflow you want to use.

The log says something about a missing path or file. Can you check which paths are used and if they are there.

For log files it might be best to set that to debug mode and attach it to your entry. Would make the text much easier to read.

3

@mlauber71 Thanks for your quick reply.
I have uploaded the workflow. All codes are visible here.
I have checked all the paths. The path and the file for sirius.pqp is there. For the error message of …/merged_osw.osw & …/scored_ms1ms2.osw the path is there but not the file.

Best regards,
Adrian

DIAMetAlyzer_AB.knwf (633.6 KB)

4

Hi!

Windows will probably not like the starting slash in the filename. I am not sure if the pipeline was tested on Windows yet. There might be some assumptions in the code for Linux/macOS.

Best wishes
Julianus

1 Like
5

Hello,

Thank you for your reply!
Then I will try to remove the slash at the beginning in the file name or adapt the code for windows. I thought that the pipeline was also tested on windows since the tutorial included a description for the windows version.
Nevertheless thank you.

Kind regards
Adrian

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