ExecMolecularParallelPairs

[hhabra]

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

[mwang87]

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

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

[hhabra]

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.

[mwang87]

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/