FeatureFinderMultiplex fails in "Peptide and Protein Quantification via Stable Isotope Labelling" workflow

FeatureFinderMultiplex constantly fails in the workflow “Peptide and Protein Quantification via Stable Isotope Labelling (SIL)”,

  • with no any specific error messages;

Job Information

Galaxy Tool ID toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.6+galaxy0
Job State error
Command Line empty
Tool Standard Output empty
Tool Standard Error empty
Tool Exit Code
Job API ID 11ac94870d0bb33a763cfd6ce92de8fd

Would you please have a look at the history and provide guidance?


Hi @qcsciphi

Thanks for sharing your history.

The problem was probably introduced when creating the fasta input. I can’t see those details since the three files are in a different history, but you can review that step. It looks like two were from some original files, and the third had a replace function run on it.

So, I would suggest back tracking to those steps to see if anything odd was done by comparing the fasta content between the tutorial data and your custom data.

Keep in mind the data content as well. If you are changing the inputs to consider, you might need to adjust parameters in the workflow as well. As a guess, the error looks like the terms used with FeatureFinderMultiplex are not a match for your custom data (the fasta, or in one of the intermediate tools), and FFM died out not knowing what to do about the conflict. Since you have access to all the files and know your goals, maybe back track and make sure all the inputs and upstream steps make sense first, then experiment with changes directly in the history until it works, and finally adjust the workflow once you know exactly what to change.

I am running the workflow on the tutorial data in here to make sure that part is actually Ok. Not quite finished but did make it farther than yours so far. So, I don’t think the workflow itself is the overall root problem. This is more about the default template workflow not being quite a fit for your custom data inputs yet. Galaxy | Europe

Hi @jennaj
Thanks for your observations and thorough description.
FeatureFinderMultiplex is only using mass spectrometry data in mzml format, and nothing else.
The part of the workflow processing the fasta input is running OK.

In FeatureFinderMultiplex, I will more focus on “algorithmic parameters” > “Labels used for labelling the samples”, where SILAC [Lys4,Arg6][Lys8,Arg10] etc. labels must be selected, as my mzml data contains labeled proteomic data.

Thanks a lot!