Classic Molecular Networking workflow not working with Bruker converted mzml files

[Giovanni911]

I tried to run a Classic Molecular Networking workflow by using a mzml file obtained by converting Bruker raw files with their in-house algorithm (using mass convert seems to not be an option since it produces a discrepancy between MS1 and MS2). However when I run these mzml files in GNPS2 it fails, and I get the following report:

Workflow execution completed unsuccessfully! The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'mscluster (1)'

Caused by: Process mscluster (1) terminated with an error exit status (1)

Command executed:

mkdir clustering python /app/workflows_user/classical_networking_workflow/bin/scripts/mscluster_wrapper.py input_spectra /app/workflows_user/classical_networking_workflow/bin/binaries spectra clustering --min_cluster_size 2 --pm_tolerance 0.02 --fragment_tolerance 0.02 --min_peak_intensity 0.0

Command exit status: 1

Command output: no pyteomics

Command error: DEBUG: main_specnets.cpp : 670: execMode = sps DEBUG: main_specnets.cpp : 671: GenoMS_FLAG=X DEBUG: main_specnets.cpp : 672: Merge_FLAG=X DEBUG: main_specnets.cpp : 674 DEBUG: main_specnets.cpp : 676: SH1:179b02ee5e6f1f067be7c3a7f51a809125d64014 DEBUG: main_specnets.cpp : 711: initialStageString = DEBUG: main_specnets.cpp : 717: finalStageString = mscluster DEBUG: main_specnets.cpp : 719: commandLineParams.getValue("SINGLE_STEP") = DEBUG: main_specnets.cpp : 727: ip.getValue("GRID_PARAMS", "XXX") = XXX DEBUG: main_specnets.cpp : 124: p.getValue("GRID_PARAMS", "XXX") = XXX DEBUG: main_specnets.cpp : 781: initialStageString = DEBUG: main_specnets.cpp : 786: initialStageString = begin DEBUG: main_specnets.cpp : 792: finalStageString = mscluster DEBUG: main_specnets.cpp : 797: finalStageString = mscluster DEBUG: ../../../trunk/StatusFile.cpp : 31: Updated program status to Running DEBUG: main_specnets.cpp : 839: initialStage = 0 DEBUG: main_specnets.cpp : 841: finalStage = 2 DEBUG: main_specnets.cpp : 848: resumeFlag = 0 DEBUG: main_specnets.cpp : 854: gridExecutionFlag = 0 DEBUG: main_specnets.cpp : 859: Spectral Networks 2.0.0: session started on: Thu May 2 09:18:49 2024

DEBUG: main_specnets.cpp : 860: Starting stage: [begin] on: Thu May 2 09:18:49 2024

DEBUG: main_specnets.cpp : 417: Made directory 'spectra' DEBUG: main_specnets.cpp : 417: Made directory 'spectra/grid_scoring' DEBUG: main_specnets.cpp : 417: Made directory 'aligns' DEBUG: main_specnets.cpp : 417: Made directory 'specnets' DEBUG: main_specnets.cpp : 417: Made directory 'homology' DEBUG: main_specnets.cpp : 417: Made directory 'homology/grid_t' DEBUG: main_specnets.cpp : 417: Made directory 'homology/grid_d' DEBUG: main_specnets.cpp : 417: Made directory 'homology/grid2_t' DEBUG: main_specnets.cpp : 417: Made directory 'homology/grid2_d' DEBUG: main_specnets.cpp : 417: Made directory 'report' DEBUG: main_specnets.cpp : 417: Made directory 'ReportData' DEBUG: main_specnets.cpp : 417: Made directory 'assembly' DEBUG: main_specnets.cpp : 927: No amino acid masses loaded. Using defaults DEBUG: main_specnets.cpp : 939 DEBUG: main_specnets.cpp : 153 DEBUG: main_specnets.cpp : 182 ERROR: main_specnets.cpp : 262: Input spectra set is empty ERROR: main_specnets.cpp : 263: Please make sure input files are 32-bit uncompressed mzXML files that contain MS/MS spectra ERROR: main_specnets.cpp : 949: Failed loading initial data. DEBUG: ../../../trunk/StatusFile.cpp : 31: Updated program status to Error

Work dir: /data/nf_data/server/nf_work/d42c12e601a444e188a77cf18fbcad86/c0/25d341221118268a40db44a4a90068

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[mwang87]

I would recommend using timsconvert

https://academic.oup.com/bioinformatics/article/38/16/4046/6618521

[Giovanni911]

I will try thanks!