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Error when importing .raw files on Mac Virtual Machine

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Error when importing .raw files on Mac Virtual Machine filippa qvist  2023-12-12 05:05
 

I recently had an issue where I got an error message (see attached image and full error text below) when I tried to import .raw files into Skyline.
For context, I was running from a MacBook Pro with a virtual machine called Parallels Desktop, and I subsequently spoke to another Mac VM user who had experienced the same issue. It happened when importing with both Skyline 23.1 and Skyline Daily.

I was able to import .mzXML and .d (TimsTOF file folders) into Skyline as normal, but when importing .raw files I encountered the error listed below. This issue was only present when the .raw files were stored in a Mac directory (\Mac\Home\Documents), but can be resolved by moving the files to either the C: drive or any network drive. In those cases, the .raw files open as normal.

I have now just changed where I store the files I want to import, but was asked to still report the error.
Thank you!

Full error:
At 1:59 PM:
Failed importing results file '\Mac\Home\Documents\GroupedStudies1\HeartFailure\raw\D_102_REP1.raw'.
[RawFileImpl::ctor()] Corrupt RAW file \Mac\Home\Documents\GroupedStudies1\HeartFailure\raw\D_102_REP1.raw
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file '\Mac\Home\Documents\GroupedStudies1\HeartFailure\raw\D_102_REP1.raw'.
[RawFileImpl::ctor()] Corrupt RAW file \Mac\Home\Documents\GroupedStudies1\HeartFailure\raw\D_102_REP1.raw ---> System.Exception: [RawFileImpl::ctor()] Corrupt RAW file \Mac\Home\Documents\GroupedStudies1\HeartFailure\raw\D_102_REP1.raw
at pwiz.CLI.msdata.ReaderList.read(String filename, MSData result, Int32 runIndex, ReaderConfig config)
at pwiz.ProteowizardWrapper.MsDataFileImpl..ctor(String path, Int32 sampleIndex, LockMassParameters lockmassParameters, Boolean simAsSpectra, Boolean srmAsSpectra, Boolean acceptZeroLengthSpectra, Boolean requireVendorCentroidedMS1, Boolean requireVendorCentroidedMS2, Boolean ignoreZeroIntensityPoints, Int32 preferOnlyMsLevel, Boolean combineIonMobilitySpectra, Boolean trimNativeId) in C:\proj\skyline_23_1\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 201
at pwiz.Skyline.Model.Results.MsDataFilePath.OpenMsDataFile(Boolean simAsSpectra, Boolean preferOnlyMs1, Boolean centroidMs1, Boolean centroidMs2, Boolean ignoreZeroIntensityPoints) in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Results\MsDataFilePath.cs:line 295
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 191
--- End of inner exception stack trace ---
 
 
Brian Pratt responded:  2023-12-12 09:19

I can think of a few things to try:

Make sure the file hasn't been changed somehow in the act of copying to the mac
Make sure you're using the latest version of Parallels
Make sure this all works on an actual Windows machine

Other than that, there's not much we can do - the code that's failing is provided by Thermo, we don't have any insight into how that operates.

Thanks for using the Skyline support board,

Brian Pratt
 
Nick Shulman responded:  2023-12-12 21:05
That is strange behavior.

I have made a special build of Skyline-daily which will give you a more verbose error message when that error happens.
You can install it from here:
https://proteome.gs.washington.edu/~nicksh/SkylineDailyPreview/
The special Skyline-daily installer has not been cryptographically signed so Windows might warn you against installing it, so you might have to hunt around for the "Run anyway" button. The special Skyline-daily will appear on the Windows Start Menu as "Skyline preview".

If you tell us what error message you see with this special build of Skyline that might give us an idea of how to fix this or who to report this bug to.
-- Nick