MSFragger error

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MSFragger error Shawn Rice  2021-12-01
 
Greetings,

I am trying to run MSFragger in Skyline and keep getting the following error. Any suggestions? I am running the newest version of Skyline-Daily (64) 21.1.9.334 (15641fb9e). The run log is attached.

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Skyline-daily
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Error
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OK More Info
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System.IO.InvalidDataException: while fixing scan numbers in PIN file, ran out of correct scan numbers from pepXML
   at pwiz.Skyline.Model.DdaSearch.MsFraggerSearchEngine.FixMSFraggerPin(String cruxInputFilepath, String cruxFixedInputFilepath, String msfraggerPepxmlFilepath) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DdaSearch\MsFraggerSearchEngine.cs:line 302
   at pwiz.Skyline.Model.DdaSearch.MsFraggerSearchEngine.Run(CancellationTokenSource cancelToken, IProgressStatus status) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DdaSearch\MsFraggerSearchEngine.cs:line 165
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Thanks,
Shawn
 
 
matt.chambers42 responded:  2021-12-02
Hi Shawn,

Thanks for testing the new capability. I haven't tested on TimsTOF data yet: the existing MSAmanda can't really deal with it so I didn't think about it when adding MSFragger. I'll try to get that fixed soon.