Spectral library error

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Spectral library error malikshagufa93  2023-05-22 16:59
 

Hi,
I am new to the Skyline and below is the error I am facing while trying build a spectral library.

System.IO.IOException: ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=11022"
ERROR: reading file OR4_110128_EDG_11EDEG002_smallSCX_26w_fr18.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=20469"
ERROR: reading file OR4_110129_EDG_11EDEG002_smallSCX_26w_fr11.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=7522"
ERROR: reading file OR4_110204_EDG_11EDEG002_smallSCX_16w_fr18.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=11924"
ERROR: reading file OR4_110204_EDG_11EDEG002_smallSCX_16w_fr20.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=7562"
ERROR: reading file OR4_110206_EDG_11EDEG002_smallSCX_16w_fr13.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=23734"
ERROR: reading file OR5_20100802_MA_EDG_ERCC1_26w_small_f20.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=16277"
ERROR: reading file OR5_201023_EDG_ERCC1_8w_small_f18.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=7780"
ERROR: reading file OR5_201023_EDG_ERCC1_8w_small_f9_2.mzid.gz
ERROR: [SpectrumList_Thermo::spectrum()] Unknown exception retrieving spectrum "controllerType=0 controllerNumber=1 scan=12722"
ERROR: reading file OR5_201029_EDG_ERCC1_16w_small_f7.mzid.gz

Command-line: C:\Windows\system32\BlibBuild -s -A -H -o -c 0.95 -i spectral_library_PXD000046 -S "C:\Users\USER\AppData\Local\Temp\tmpA768.tmp" "Z:\MS_raw\PeptideAtlas\Mouse_2016-01-JP\PXD000046\spectral_library_PXD000046.redundant.blib"
Working directory: Z:\MS_raw\PeptideAtlas\Mouse_2016-01-JP\PXD000046
위치: pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) 파일 C:\proj\skyline_22_2\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:줄 161
위치: pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) 파일 C:\proj\skyline_22_2\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:줄 412
위치: pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) 파일 C:\proj\skyline_22_2\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:줄 161

Please help at the earliest.

 
 
Nick Shulman responded:  2023-05-22 17:05
It looks like it is having trouble reading the .raw files associated with those .mzid files.

Do you have a file on your computer called "OR4_110128_EDG_11EDEG002_smallSCX_26w_fr18.raw"?
I am thinking that must be the file that BiblioSpec was trying to read spectra from when it was processing the search result file "OR4_110128_EDG_11EDEG002_smallSCX_26w_fr18.mzid.gz".

Please send us the following files:
OR4_110128_EDG_11EDEG002_smallSCX_26w_fr18.mzid.gz
OR4_110128_EDG_11EDEG002_smallSCX_26w_fr18.raw

You can upload the files here:
https://skyline.ms/files.url

-- Nick
 
malikshagufa93 responded:  2023-05-22 19:49
Hi,
I have uploaded the file. Please check.
 
Nick Shulman responded:  2023-05-23 12:42
Thank you for uploading those files.
I will try to figure out what might have gone wrong for you, but I might not be able to figure it out.

Could you send us some screenshots showing the steps that you went through in Skyline? That might help us figure out what you were doing when you got the errors that you got.
-- Nick