FBMN Error

[Nikki A.]

IF YOU ARE REPORTING AN ISSUE, PLEASE MAKE SURE:

1. Your questions was not addressed previously in the GNPS FORUM.

2. Is not already reported in our GitHub repository : https://github.com/CCMS-UCSD/GNPS_Workflows.

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===> if the problem couldn't be solved:

Create a post on the GNPS forum or an issue on GitHub. Include the GNPS URL link to the job(s). Specify the mass spectrometer type and manufacturer, as well as the procedure for data conversion to mzML/mzXML. If this is relevant for the issue/discussion, indicate the experimental conditions (chromatography, ionisation mode, MS/MS acquisition parameters, ...).

I am trying to use FBMN to visualize a dataset with the blanks excluded, after having already successfully run the same dataset with the blanks, and my new jobs are failing with the following error:
Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_23/scripts/filter_spectra.py", line 29, in <module> max_scan = max(included_scans) ValueError: max() arg is an empty sequence Tool execution terminates abnormally with exit code [1]

I preprocessed in MZMine and exported the same way I always have for GNPS and this is the first time it is failing like this for me. It is failing in the two separate jobs linked below.

 http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=395eaca5c4be4ccbb2a248af6a9e75e8

 http://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=9b3afe7af0d54fff9b7044f3afba2908

Is anyone else having this same issue or know how to fix it?

[Mingxun Wang]

Its seems you input does not have any MS2 spectra in the MGF. 

Perhaps you have adjusted your parameters to be too strict. 

Ming