GNPSDocumentation ExecMolecularParallelPairs

I have gone through tortoruous hours of trying to overcome vague error after vague error within GNPS FBMN. I have reached this error and I have no idea what I can do to overcome this. I have attached the .mgf file [remade as a .txt to allow for Github upload], the feature table, and a metadata table. The error I get is:

DEBUG: main_execmodule.cpp : 154 DEBUG: ExecSpecProtAlign.cpp : 219 DEBUG: ExecSpecTagGen.cpp : 20 DEBUG: ExecSpecTagGen.cpp : 20 DEBUG: ExecPenaltyGen.cpp : 26 DEBUG: ExecPenaltyGen.cpp : 26 DEBUG: main_execmodule.cpp : 158 DEBUG: main_execmodule.cpp : 169 DEBUG: main_execmodule.cpp : 179: jobDoneFile = ExecMolecularParallelPairs__results.param DEBUG: main_execmodule.cpp : 228: NORMAL EXECUTION DEBUG: main_execmodule.cpp : 229 DEBUG: ExecMolecularParallelPairs.cpp : 174: Loading MS2 spectra.. spectra_filtered/specs_ms.mgf DEBUG: ExecMolecularParallelPairs.cpp : 176: Could not load spectra_filtered/specs_ms.mgf ERROR: main_execmodule.cpp : 232: Loading input data for module of type [ExecMolecularParallelPairs] DEBUG: ExecSpecProtAlign.cpp : 219 Tool execution terminates abnormally with exit code [252]

Please help.

RP_POS_gnps_metadata.tsv RP_POS_gnps_output_v6.tsv RP_POS_gnps_output.mgf.txt

Oct 14 '25 05:10 hhabra

My recommendation is to checkout these workflows, these might be more helpful:

https://github.com/Wang-Bioinformatics-Lab/GNPS2_Workflows

Oct 14 '25 17:10 mwang87

I would use GNPS2, but I have no idea how to get an access token to create an account... and I'm sure I'm not alone.

Oct 14 '25 23:10 hhabra

Oh the above is the source code - you can run those pipelines on your own computer if you'd wish.

As for accounts, i think this will help: https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/accounts/

Oct 14 '25 23:10 mwang87