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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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philosopher pipeline does not run through - only if steps started separately #530

Closed fstein closed 3 years ago

fstein commented 3 years ago

Hi,

I tried to set up the pipeline for running msfragger and philosopher. When I do this, I stops after the Protein Inference step. If I then modify the parameter.yml file and set only one step to yes to be executed, the analysis does finish if I execute it in the following order: FDR Filtering: Label-Free Quantification Isobaric Quantification Individual Reports Integrated Reports

I have a TMT11 plex experiment (1 raw file which I converted to an mzML file with the following command: 'msconvert" *.raw --mzML --64 --zlib --filter "peak philosopher.yml.txt Picking true 1-"'

I attached my parameter file. I also have another issue: When trying to print the philosopher.yml file using the "philosopher pipeline --print" command, it would print me a philosopher.yml file from version Version 3.6.0. The latest version is 4.0.1. If I use the Version 3.6.0, the pipeline complains alot about missing parameter.

Thanks for your help.

Cheers,

Frank

fstein commented 3 years ago

Sorry, just realized that it's probably the wrong location to ask. I will ask again at Nesvilab/Philosopher.

sarah-haynes commented 3 years ago

moved to https://github.com/Nesvilab/philosopher/issues/289