Failure imorting mzXML cfarnsworth  2019-05-02 06:30
 

I get the following message when trying to import mzXML files. Note only 6 of 24 files in total failed.
Thanks, Charles

Failed importing results file 'D:\IMAC Keezer\180418_28574_CF_x.mzXML'.
Object reference not set to an instance of an object.

Inner exceptions:
Exception type: System.NullReferenceException
Error message: Object reference not set to an instance of an object.
Object reference not set to an instance of an object.
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.get_PercentComplete() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 806
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.UpdatePercentComplete() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 599
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 587
at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 77
at pwiz.Skyline.Model.Results.ChromDataSet.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 233
at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 144
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 452
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263
 
 
Brian Pratt responded:  2019-05-02 09:06
Hi Charles,

Thanks for the report.

Have you tried opening the mzXML file in a viewer like ProteoWizard SeeMS to verify that it's not corrupted in some manner?

If that's not the issue, can you provide the Skyline document (File > Share > Complete) and an mzXML file sufficient to demonstrate the problem?

Thanks,

Brian Pratt
 
Brian Pratt responded:  2019-05-02 09:47
Actually, we'd like to see your .sky.zip and .mzXML files even if the mzXML is corrupt - we'd prefer to be more graceful in handling that condition.

Thanks

Brian
 
Brendan MacLean responded:  2019-05-02 10:06
Ideally just one mzXML file, if it can be made to reliably fail in this way in isolation. If the failure is more complicated than single file failure, please explain and provide the necessary files to reproduce the failure.