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Bruker qTOF .d amyzheng  2026-01-28 15:33
 

Dear Skyline team,

I am loading files into skyline version 25.1.0.237 64-bit. Every time I load in files, a few of them give me a loading error. Usually the error clears after retry. Is there a way to prevent these files from generating the error?

At 3:22 PM:
Failed importing results file 'E:\UBC_work\Kidney_MostafaAhmed_porject\Lipid+\All_files_MS-Dial\Sample_42_B-C5_1_8422.d'.
error reading spectrum scan=4648
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\UBC_work\Kidney_MostafaAhmed_porject\Lipid+\All_files_MS-Dial\Sample_42_B-C5_1_8422.d'.
error reading spectrum scan=4648 ---> System.Reflection.TargetInvocationException: error reading spectrum scan=4648 ---> System.Exception: error reading spectrum scan=4648 ---> System.Exception: SQLITE_IOERR[10]: disk I/O error
at pwiz.CLI.msdata.SpectrumList.spectrum(Int32 index, DetailLevel detailLevel)
at pwiz.ProteowizardWrapper.MsDataFileImpl.GetCachedSpectrum(Int32 scanIndex, DetailLevel detailLevel) in C:\proj\skyline_25_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 1404
at pwiz.ProteowizardWrapper.MsDataFileImpl.GetSpectrum(Int32 spectrumIndex) in C:\proj\skyline_25_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 995
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1112
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.ReadSpectrum(Int32& i) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1163
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.Read() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 990
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.<RunAsync>b__33_0() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 848
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Util\Util.cs:line 1926
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.NextSpectrum() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 953
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 274
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 254
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 620
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 395
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_25_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263
--- End of inner exception stack trace ---
 
 
Brian Pratt responded:  2026-01-28 17:13

Is that a network drive, perhaps? Those can be flaky. You might try using a local copy, though that’s not very convenient of course.
 
amyzheng responded:  2026-01-29 09:45

Hi Brian,

My raw data files are currently saved to a SSD external hard-drive.
 
Brian Pratt (Claude) responded:  2026-01-29 13:14

So that's really a hardware problem, but it certainly would be nice if the ProteoWizard file reader library could do a retry. I'll put that on our to-do list.

In the meantime, it's possible that your PC has some USB ports that are faster than others (USB 3 vs USB 2) - with non-USB-C ports you can look for the blue ones, they should be USB 3.

Brian