PD 2.4 Node installation error

im281 commented 3 years ago

Any ideas?

huiyinc commented 3 years ago

Hi,

Do you install MSFraggerPDv24 via Proteome Discoverer? Or do you install it via the command line?

Huiyin

im281 @.***> 於 2021年5月24日週一上午3:29寫道：

Any ideas? [image: image] https://user-images.githubusercontent.com/10081392/119273986-206bfc80-bbfd-11eb-94cc-59d3daf25ee7.png

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

im281 commented 3 years ago

I did it both ways. Is the command Maggellan.Server.exe -install? I also did 'scan for missing features' and got the same error

huiyinc commented 3 years ago

Hi,

Is it possible to send me the MagellanServer.log so I can check what the issue is? You may find the log file at: C:\ProgramData\Thermo\Proteome Discoverer 2.4\ Logs Thanks.

Huiyin

im281 @.***> 於 2021年5月25日週二上午8:05寫道：

I did it both ways. Is the command Maggellan.Server.exe -install? I also did 'scan for missing features' and got the same error

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

im281 commented 3 years ago

2021-05-23 22:22:29,258 INFO [1] ShellApplication - Thermo.Discoverer (2.4.1.15, x64) started at 5/23/2021 10:22:29 PM on EC2AMAZ-VON3CTF [8 CPUs] running Microsoft Windows NT 6.2.9200.0 (64bit) [.NET: 4.0.30319.42000] in the context of user Administrator 2021-05-23 22:22:29,963 WARN [7] SafeDirectoryCatalog - Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) System.IO.FileLoadException: Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.Assembly.Load(AssemblyName assemblyRef) at System.ComponentModel.Composition.Hosting.AssemblyCatalog.LoadAssembly(String codeBase) at System.ComponentModel.Composition.Hosting.AssemblyCatalog..ctor(String codeBase, ICompositionElement definitionOrigin) at Infrastructure.Composite.Catalogs.SafeDirectoryCatalog.CreateAssemblyCatalogGuarded(String assemblyFilePath)

2021-05-23 22:22:30,888 DEBUG [1] CompositionContainerFactory - Creating CompositionContainer took 1.5 s. 2021-05-23 22:22:31,189 DEBUG [1] ServerConfigurationManager - Reading configuration files 2021-05-23 22:22:31,349 WARN [1] SpectrumFileFactory - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.SpectrumFileFactory.a()

2021-05-23 22:22:31,498 DEBUG [1] SpectrumFileFactory - Finding 3 spectrum exporter and 6 spectrum importer took 224.8 ms. 2021-05-23 22:22:31,666 DEBUG [1] GroupRepository - GroupRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] UserRepository - UserRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] ShellApplication - Loading remote configuration from 'C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\Config\RemotingClient.config'. 2021-05-23 22:22:31,751 DEBUG [1] LicenseLoggerFacade - Creating TransactionLicenseManager. 2021-05-23 22:22:31,930 DEBUG [1] LicenseLoggerFacade - Assembly=ThermoFisher.Licensing, Version=1.0.17.0, Culture=neutral, PublicKeyToken=null 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FNP_Act_Installer.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FnpCommsSoap.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.dll, Version=1.0.0.1 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.libFNP.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - Is64BitOS=True, Is64BitProcess=True, IsVM=True, IsInternetAvailable=True, OS Version=Microsoft Windows NT 6.2.9200.0, MachineName=EC2AMAZ-VON3CTF 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Subdirectory: Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Data Directory: C:\ProgramData\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common User Settings Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Templates Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Filter Sets Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\FilterSets 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Layouts Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\Layouts 2021-05-23 22:22:35,328 WARN [1] LicenseManager - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.LicenseManager.b()

2021-05-23 22:22:35,366 INFO [1] ShellApplication - Retrieving licensing information took 101.4 ms 2021-05-23 22:22:36,219 DEBUG [1] SessionManager - Session activated for " (Administrator)". 2021-05-23 22:22:36,219 INFO [1] CommonGateway - 22:22:36 - User:administrator successfully logged in 2021-05-23 22:22:36,324 DEBUG [1] ModuleController - Starting 2021-05-23 22:22:36,440 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options on parent! 2021-05-23 22:22:36,786 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options docked! 2021-05-23 22:22:40,686 DEBUG [1] ServerAccessService - User: Administrator attempts to login at server: localhost 2021-05-23 22:22:41,721 INFO [8] ModuleController - Preparing Study Loading took 2 ms. 2021-05-23 22:22:42,154 INFO [1] ModuleController - Show start page 2021-05-23 22:23:53,605 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 1. Available Memory: 26345/32767 MB 2021-05-23 22:23:54,651 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:54,684 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:55,163 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:55,252 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:23:55,268 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 14 ms 2021-05-23 22:23:55,283 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:55,305 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1687 ms 2021-05-23 22:23:56,285 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:56,295 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:56,315 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:56,327 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:23:56,376 ERROR [1] StudyManagerWorkItemController - Create new study failed: Could not find a part of the path. System.IO.DirectoryNotFoundException: Could not find a part of the path. at System.IO.Error.WinIOError(Int32 errorCode, String maybeFullPath) at System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.PersistStudyToXmlFile(String fileName, Boolean createBackup, CancellationToken token) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.SaveStudyToFile(String fileName) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.CreateNewStudy(String studyFileName, String studiesDirectory, String studyTemplateFileName, QuanMethod quanMethod, Boolean remote) at Thermo.Discoverer.WorkflowEditorModule.StudyManagerWorkItemController.d56.MoveNext() 2021-05-23 22:23:58,557 ERROR [1] WindowsFormsMessageService - Message: Create new study failed: Could not find a part of the path.; Result: OK 2021-05-23 22:25:08,170 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 2. Available Memory: 26268/32767 MB 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:09,253 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:09,282 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:25:09,282 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 2 ms 2021-05-23 22:25:09,286 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:09,326 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1153 ms 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:10,337 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:10,356 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:10,391 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:25:34,691 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:37:16,229 INFO [1] DataSequenceStarter - Start submitting of 1 analysis sequences... 2021-05-23 22:37:16,350 INFO [17] DataSequenceStarter - Found 0 of 3 files on the server. 2021-05-23 22:37:19,027 INFO [6] DataSequenceStarter - Found 1 of 1 files on the server. 2021-05-23 22:37:19,764 INFO [1] DataSequenceStarter - Submitting analysis sequence took 3534 ms (Workflow: TargetedDiscovery, Result Filename: E:\5kProteinProject_20210512\20210515\studies\RC5 30min PharmaF Baseline\TESTING_202100523_RC5_30min-PharmaF_50cm_TE-DDA-Baseline.pdResult). 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Requesting new exclusive token source 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Creating new exclusive token source 2021-05-23 22:37:19,882 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:37:19,911 DEBUG [1] AdminViewWorkItemController - Starting 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Setting directories: Current directory '', new directory '' 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Directories were set: Current directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, new directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, enabled True 2021-05-23 22:37:20,773 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 23:13:07,871 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 23:13:42,030 INFO [1] WindowsFormsMessageService - Message: You changed the file directory to E:\Scratch. The change will be applied when Proteome Discoverer starts next time. Do you want to save the changes?; Result: Yes 2021-05-23 23:13:42,339 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory E:\Scratch, enabled True 2021-05-23 23:13:48,296 INFO [1] ShellApplication - Closing shell. 2021-05-23 23:13:48,438 INFO [1] ShellApplication - Request server shut down. 2021-05-23 23:13:49,151 DEBUG [1] ShellApplication - Closing server took 711 ms 2021-05-23 23:13:49,348 DEBUG [1] AdminViewWorkItemController - Terminating 2021-05-23 23:13:49,462 DEBUG [1] StudyManagerWorkItemController - Open studies (after close): 1. Available Memory: 26220/32767 MB 2021-05-23 23:13:49,615 DEBUG [1] ShellApplication - Close server from Main

im281 commented 3 years ago

Any ideas? I think it might be a 32 bit vs 64 bit issue?

huiyinc commented 3 years ago

Hi,

One possibility is that the MSFraggerPDv24.dll is blocked due to the security of Windows system. You may try the following solutions and see if they work.

Please check that (1) you have .Net 4.7 or above installed in your computer, (2) the “MSFraggerPDv2x.dll” file is not blocked by your operating system. To unblock it, right click on the file and select ‘Properties’, then in the ‘Attributes’ section, select ‘Advanced’ and then click ‘Unblock’. Alternatively, you can run unblock-file -path "C:\Program Files\Thermo\Proteome Discoverer 2.x\System\Release\MSFraggerPDv2x.dll" (make sure this path is correct) from Windows PowerShell as administrator.

Thanks.

Huiyin

im281 @.***> 於 2021年5月25日下午9:53 寫道：

2021-05-23 22:22:29,258 INFO [1] ShellApplication - Thermo.Discoverer (2.4.1.15, x64) started at 5/23/2021 10:22:29 PM on EC2AMAZ-VON3CTF [8 CPUs] running Microsoft Windows NT 6.2.9200.0 (64bit) [.NET: 4.0.30319.42000] in the context of user Administrator 2021-05-23 22:22:29,963 WARN [7] SafeDirectoryCatalog - Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) System.IO.FileLoadException: Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.Assembly.Load(AssemblyName assemblyRef) at System.ComponentModel.Composition.Hosting.AssemblyCatalog.LoadAssembly(String codeBase) at System.ComponentModel.Composition.Hosting.AssemblyCatalog..ctor(String codeBase, ICompositionElement definitionOrigin) at Infrastructure.Composite.Catalogs.SafeDirectoryCatalog.CreateAssemblyCatalogGuarded(String assemblyFilePath)

2021-05-23 22:22:30,888 DEBUG [1] CompositionContainerFactory - Creating CompositionContainer took 1.5 s. 2021-05-23 22:22:31,189 DEBUG [1] ServerConfigurationManager - Reading configuration files 2021-05-23 22:22:31,349 WARN [1] SpectrumFileFactory - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.SpectrumFileFactory.a()

2021-05-23 22:22:31,498 DEBUG [1] SpectrumFileFactory - Finding 3 spectrum exporter and 6 spectrum importer took 224.8 ms. 2021-05-23 22:22:31,666 DEBUG [1] GroupRepository - GroupRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] UserRepository - UserRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] ShellApplication - Loading remote configuration from 'C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\Config\RemotingClient.config'. 2021-05-23 22:22:31,751 DEBUG [1] LicenseLoggerFacade - Creating TransactionLicenseManager. 2021-05-23 22:22:31,930 DEBUG [1] LicenseLoggerFacade - Assembly=ThermoFisher.Licensing, Version=1.0.17.0, Culture=neutral, PublicKeyToken=null 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FNP_Act_Installer.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FnpCommsSoap.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.dll, Version=1.0.0.1 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.libFNP.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - Is64BitOS=True, Is64BitProcess=True, IsVM=True, IsInternetAvailable=True, OS Version=Microsoft Windows NT 6.2.9200.0, MachineName=EC2AMAZ-VON3CTF 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Subdirectory: Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Data Directory: C:\ProgramData\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common User Settings Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Templates Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Filter Sets Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\FilterSets 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Layouts Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\Layouts 2021-05-23 22:22:35,328 WARN [1] LicenseManager - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.LicenseManager.b()

2021-05-23 22:22:35,366 INFO [1] ShellApplication - Retrieving licensing information took 101.4 ms 2021-05-23 22:22:36,219 DEBUG [1] SessionManager - Session activated for " (Administrator)". 2021-05-23 22:22:36,219 INFO [1] CommonGateway - 22:22:36 - User:administrator successfully logged in 2021-05-23 22:22:36,324 DEBUG [1] ModuleController - Starting 2021-05-23 22:22:36,440 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options on parent! 2021-05-23 22:22:36,786 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options docked! 2021-05-23 22:22:40,686 DEBUG [1] ServerAccessService - User: Administrator attempts to login at server: localhost 2021-05-23 22:22:41,721 INFO [8] ModuleController - Preparing Study Loading took 2 ms. 2021-05-23 22:22:42,154 INFO [1] ModuleController - Show start page 2021-05-23 22:23:53,605 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 1. Available Memory: 26345/32767 MB 2021-05-23 22:23:54,651 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:54,684 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:55,163 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:55,252 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:23:55,268 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 14 ms 2021-05-23 22:23:55,283 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:55,305 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1687 ms 2021-05-23 22:23:56,285 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:56,295 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:56,315 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:56,327 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:23:56,376 ERROR [1] StudyManagerWorkItemController - Create new study failed: Could not find a part of the path. System.IO.DirectoryNotFoundException: Could not find a part of the path. at System.IO.Error.WinIOError(Int32 errorCode, String maybeFullPath) at System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.PersistStudyToXmlFile(String fileName, Boolean createBackup, CancellationToken token) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.SaveStudyToFile(String fileName) at Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.CreateNewStudy(String studyFileName, String studiesDirectory, String studyTemplateFileName, QuanMethod quanMethod, Boolean remote) at Thermo.Discoverer.WorkflowEditorModule.StudyManagerWorkItemController.d56.MoveNext() 2021-05-23 22:23:58,557 ERROR [1] WindowsFormsMessageService - Message: Create new study failed: Could not find a part of the path.; Result: OK 2021-05-23 22:25:08,170 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 2. Available Memory: 26268/32767 MB 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:09,253 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:09,282 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:25:09,282 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 2 ms 2021-05-23 22:25:09,286 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:09,326 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1153 ms 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:10,337 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:10,356 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:10,391 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:25:34,691 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:37:16,229 INFO [1] DataSequenceStarter - Start submitting of 1 analysis sequences... 2021-05-23 22:37:16,350 INFO [17] DataSequenceStarter - Found 0 of 3 files on the server. 2021-05-23 22:37:19,027 INFO [6] DataSequenceStarter - Found 1 of 1 files on the server. 2021-05-23 22:37:19,764 INFO [1] DataSequenceStarter - Submitting analysis sequence took 3534 ms (Workflow: TargetedDiscovery, Result Filename: E:\5kProteinProject_20210512\20210515\studies\RC5 30min PharmaF Baseline\TESTING_202100523_RC5_30min-PharmaF_50cm_TE-DDA-Baseline.pdResult). 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Requesting new exclusive token source 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Creating new exclusive token source 2021-05-23 22:37:19,882 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:37:19,911 DEBUG [1] AdminViewWorkItemController - Starting 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Setting directories: Current directory '', new directory '' 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Directories were set: Current directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, new directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, enabled True 2021-05-23 22:37:20,773 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 23:13:07,871 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 23:13:42,030 INFO [1] WindowsFormsMessageService - Message: You changed the file directory to E:\Scratch. The change will be applied when Proteome Discoverer starts next time. Do you want to save the changes?; Result: Yes 2021-05-23 23:13:42,339 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory E:\Scratch, enabled True 2021-05-23 23:13:48,296 INFO [1] ShellApplication - Closing shell. 2021-05-23 23:13:48,438 INFO [1] ShellApplication - Request server shut down. 2021-05-23 23:13:49,151 DEBUG [1] ShellApplication - Closing server took 711 ms 2021-05-23 23:13:49,348 DEBUG [1] AdminViewWorkItemController - Terminating 2021-05-23 23:13:49,462 DEBUG [1] StudyManagerWorkItemController - Open studies (after close): 1. Available Memory: 26220/32767 MB 2021-05-23 23:13:49,615 DEBUG [1] ShellApplication - Close server from Main

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/20#issuecomment-847889350, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA5LOGMPOMFIJO4WUYDTPOTUPANCNFSM45MACL3Q .

im281 commented 3 years ago

Any update on this?

huiyinc commented 3 years ago

Hi,

I have replied a solution for you. Does it work for you?

Huiyin

im281 @.***> 於 2021年6月29日上午6:30 寫道：

Any update on this?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/20#issuecomment-870089281, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA52K3DE5PK2ZCGG3C3TVDZYXANCNFSM45MACL3Q .

im281 commented 2 years ago

Let me try it

im281 commented 2 years ago

Thank you that worked!

On Wed, May 26, 2021 at 7:02 PM chuiyin @.***> wrote:

Hi,

One possibility is that the MSFraggerPDv24.dll is blocked due to the security of Windows system. You may try the following solutions and see if they work.

Please check that (1) you have .Net 4.7 or above installed in your computer, (2) the “MSFraggerPDv2x.dll” file is not blocked by your operating system. To unblock it, right click on the file and select ‘Properties’, then in the ‘Attributes’ section, select ‘Advanced’ and then click ‘Unblock’. Alternatively, you can run unblock-file -path "C:\Program Files\Thermo\Proteome Discoverer 2.x\System\Release\MSFraggerPDv2x.dll" (make sure this path is correct) from Windows PowerShell as administrator.

Thanks.

Huiyin

im281 @.***> 於 2021年5月25日下午9:53 寫道：

2021-05-23 22:22:29,258 INFO [1] ShellApplication - Thermo.Discoverer (2.4.1.15, x64) started at 5/23/2021 10:22:29 PM on EC2AMAZ-VON3CTF [8 CPUs] running Microsoft Windows NT 6.2.9200.0 (64bit) [.NET: 4.0.30319.42000] in the context of user Administrator 2021-05-23 22:22:29,963 WARN [7] SafeDirectoryCatalog - Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) System.IO.FileLoadException: Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.Assembly.Load(AssemblyName assemblyRef) at

System.ComponentModel.Composition.Hosting.AssemblyCatalog.LoadAssembly(String codeBase) at System.ComponentModel.Composition.Hosting.AssemblyCatalog..ctor(String codeBase, ICompositionElement definitionOrigin) at

Infrastructure.Composite.Catalogs.SafeDirectoryCatalog.CreateAssemblyCatalogGuarded(String assemblyFilePath)

2021-05-23 22:22:30,888 DEBUG [1] CompositionContainerFactory - Creating CompositionContainer took 1.5 s. 2021-05-23 22:22:31,189 DEBUG [1] ServerConfigurationManager - Reading configuration files 2021-05-23 22:22:31,349 WARN [1] SpectrumFileFactory - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.SpectrumFileFactory.a()

2021-05-23 22:22:31,498 DEBUG [1] SpectrumFileFactory - Finding 3 spectrum exporter and 6 spectrum importer took 224.8 ms. 2021-05-23 22:22:31,666 DEBUG [1] GroupRepository - GroupRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] UserRepository - UserRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] ShellApplication - Loading remote configuration from 'C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\Config\RemotingClient.config'. 2021-05-23 22:22:31,751 DEBUG [1] LicenseLoggerFacade - Creating TransactionLicenseManager. 2021-05-23 22:22:31,930 DEBUG [1] LicenseLoggerFacade - Assembly=ThermoFisher.Licensing, Version=1.0.17.0, Culture=neutral, PublicKeyToken=null 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FNP_Act_Installer.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FnpCommsSoap.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.dll, Version=1.0.0.1 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.libFNP.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - Is64BitOS=True, Is64BitProcess=True, IsVM=True, IsInternetAvailable=True, OS Version=Microsoft Windows NT 6.2.9200.0, MachineName=EC2AMAZ-VON3CTF 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Subdirectory: Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Data Directory: C:\ProgramData\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common User Settings Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Templates Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Filter Sets Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\FilterSets 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Layouts Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\Layouts 2021-05-23 22:22:35,328 WARN [1] LicenseManager - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.LicenseManager.b()

2021-05-23 22:22:35,366 INFO [1] ShellApplication - Retrieving licensing information took 101.4 ms 2021-05-23 22:22:36,219 DEBUG [1] SessionManager - Session activated for " (Administrator)". 2021-05-23 22:22:36,219 INFO [1] CommonGateway - 22:22:36 - User:administrator successfully logged in 2021-05-23 22:22:36,324 DEBUG [1] ModuleController - Starting 2021-05-23 22:22:36,440 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options on parent! 2021-05-23 22:22:36,786 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options docked! 2021-05-23 22:22:40,686 DEBUG [1] ServerAccessService - User: Administrator attempts to login at server: localhost 2021-05-23 22:22:41,721 INFO [8] ModuleController - Preparing Study Loading took 2 ms. 2021-05-23 22:22:42,154 INFO [1] ModuleController - Show start page 2021-05-23 22:23:53,605 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 1. Available Memory: 26345/32767 MB 2021-05-23 22:23:54,651 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:54,684 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:55,163 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:55,252 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:23:55,268 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 14 ms 2021-05-23 22:23:55,283 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:55,305 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1687 ms 2021-05-23 22:23:56,285 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:56,295 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:56,315 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:56,327 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:23:56,376 ERROR [1] StudyManagerWorkItemController - Create new study failed: Could not find a part of the path. System.IO.DirectoryNotFoundException: Could not find a part of the path. at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath) at System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.PersistStudyToXmlFile(String fileName, Boolean createBackup, CancellationToken token) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.SaveStudyToFile(String fileName) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.CreateNewStudy(String studyFileName, String studiesDirectory, String studyTemplateFileName, QuanMethod quanMethod, Boolean remote) at

Thermo.Discoverer.WorkflowEditorModule.StudyManagerWorkItemController.d__56.MoveNext() 2021-05-23 22:23:58,557 ERROR [1] WindowsFormsMessageService - Message: Create new study failed: Could not find a part of the path.; Result: OK 2021-05-23 22:25:08,170 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 2. Available Memory: 26268/32767 MB 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:09,253 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:09,282 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:25:09,282 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 2 ms 2021-05-23 22:25:09,286 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:09,326 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1153 ms 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:10,337 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:10,356 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:10,391 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:25:34,691 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:37:16,229 INFO [1] DataSequenceStarter - Start submitting of 1 analysis sequences... 2021-05-23 22:37:16,350 INFO [17] DataSequenceStarter - Found 0 of 3 files on the server. 2021-05-23 22:37:19,027 INFO [6] DataSequenceStarter - Found 1 of 1 files on the server. 2021-05-23 22:37:19,764 INFO [1] DataSequenceStarter - Submitting analysis sequence took 3534 ms (Workflow: TargetedDiscovery, Result Filename: E:\5kProteinProject_20210512\20210515\studies\RC5 30min PharmaF

Baseline\TESTING_202100523_RC5_30min-PharmaF_50cm_TE-DDA-Baseline.pdResult). 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Requesting new exclusive token source 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Creating new exclusive token source 2021-05-23 22:37:19,882 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:37:19,911 DEBUG [1] AdminViewWorkItemController - Starting 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Setting directories: Current directory '', new directory '' 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Directories were set: Current directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, new directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, enabled True 2021-05-23 22:37:20,773 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 23:13:07,871 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 23:13:42,030 INFO [1] WindowsFormsMessageService - Message: You changed the file directory to E:\Scratch. The change will be applied when Proteome Discoverer starts next time. Do you want to save the changes?; Result: Yes 2021-05-23 23:13:42,339 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory E:\Scratch, enabled True 2021-05-23 23:13:48,296 INFO [1] ShellApplication - Closing shell. 2021-05-23 23:13:48,438 INFO [1] ShellApplication - Request server shut down. 2021-05-23 23:13:49,151 DEBUG [1] ShellApplication - Closing server took 711 ms 2021-05-23 23:13:49,348 DEBUG [1] AdminViewWorkItemController - Terminating 2021-05-23 23:13:49,462 DEBUG [1] StudyManagerWorkItemController - Open studies (after close): 1. Available Memory: 26220/32767 MB 2021-05-23 23:13:49,615 DEBUG [1] ShellApplication - Close server from Main

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im281 commented 2 years ago

MSFragger DLL registered as PD node (Unblock under properties on DLL)

huiyinc commented 2 years ago

No problem!

Huiyin

im281 @.***> 於 2021年7月13日週二上午10:08寫道：

Thank you that worked!

On Wed, May 26, 2021 at 7:02 PM chuiyin @.***> wrote:

Hi,

One possibility is that the MSFraggerPDv24.dll is blocked due to the security of Windows system. You may try the following solutions and see if they work.

Please check that (1) you have .Net 4.7 or above installed in your computer, (2) the “MSFraggerPDv2x.dll” file is not blocked by your operating system. To unblock it, right click on the file and select ‘Properties’, then in the ‘Attributes’ section, select ‘Advanced’ and then click ‘Unblock’. Alternatively, you can run unblock-file -path "C:\Program Files\Thermo\Proteome Discoverer 2.x\System\Release\MSFraggerPDv2x.dll" (make sure this path is correct) from Windows PowerShell as administrator.

Thanks.

Huiyin

im281 @.***> 於 2021年5月25日下午9:53 寫道：

2021-05-23 22:22:29,258 INFO [1] ShellApplication - Thermo.Discoverer (2.4.1.15, x64) started at 5/23/2021 10:22:29 PM on EC2AMAZ-VON3CTF [8 CPUs] running Microsoft Windows NT 6.2.9200.0 (64bit) [.NET: 4.0.30319.42000] in the context of user Administrator 2021-05-23 22:22:29,963 WARN [7] SafeDirectoryCatalog - Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) System.IO.FileLoadException: Could not load file or assembly 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'MSFraggerPDv24, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.Assembly.Load(AssemblyName assemblyRef) at

System.ComponentModel.Composition.Hosting.AssemblyCatalog.LoadAssembly(String codeBase) at System.ComponentModel.Composition.Hosting.AssemblyCatalog..ctor(String codeBase, ICompositionElement definitionOrigin) at

Infrastructure.Composite.Catalogs.SafeDirectoryCatalog.CreateAssemblyCatalogGuarded(String assemblyFilePath)

2021-05-23 22:22:30,888 DEBUG [1] CompositionContainerFactory - Creating CompositionContainer took 1.5 s. 2021-05-23 22:22:31,189 DEBUG [1] ServerConfigurationManager - Reading configuration files 2021-05-23 22:22:31,349 WARN [1] SpectrumFileFactory - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.SpectrumFileFactory.a()

2021-05-23 22:22:31,498 DEBUG [1] SpectrumFileFactory - Finding 3 spectrum exporter and 6 spectrum importer took 224.8 ms. 2021-05-23 22:22:31,666 DEBUG [1] GroupRepository - GroupRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] UserRepository - UserRepository GetAll: Loading all DomainObjects 2021-05-23 22:22:31,682 DEBUG [1] ShellApplication - Loading remote configuration from 'C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\Config\RemotingClient.config'. 2021-05-23 22:22:31,751 DEBUG [1] LicenseLoggerFacade - Creating TransactionLicenseManager. 2021-05-23 22:22:31,930 DEBUG [1] LicenseLoggerFacade - Assembly=ThermoFisher.Licensing, Version=1.0.17.0, Culture=neutral, PublicKeyToken=null 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FNP_Act_Installer.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\FnpCommsSoap.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.dll, Version=1.0.0.1 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\ThermoFisher.Licensing.Interop.libFNP.dll, Version=11.11.1.2 build 134011 2021-05-23 22:22:31,952 DEBUG [1] LicenseLoggerFacade - Is64BitOS=True, Is64BitProcess=True, IsVM=True, IsInternetAvailable=True, OS Version=Microsoft Windows NT 6.2.9200.0, MachineName=EC2AMAZ-VON3CTF 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Subdirectory: Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Application Data Directory: C:\ProgramData\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common User Settings Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Templates Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Filter Sets Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\FilterSets 2021-05-23 22:22:35,266 INFO [1] DiscovererConfigService - Common Layouts Directory: C:\Users\Public\Documents\Thermo\Proteome Discoverer 2.4\Common Templates\Layouts 2021-05-23 22:22:35,328 WARN [1] LicenseManager - Could not load this assembly "MSFraggerPDv24.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 2.4\System\Release\MSFraggerPDv24.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information. at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks) at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark) at System.Reflection.Assembly.LoadFrom(String assemblyFile) at Thermo.Magellan.Services.LicenseManager.b()

2021-05-23 22:22:35,366 INFO [1] ShellApplication - Retrieving licensing information took 101.4 ms 2021-05-23 22:22:36,219 DEBUG [1] SessionManager - Session activated for " (Administrator)". 2021-05-23 22:22:36,219 INFO [1] CommonGateway - 22:22:36 - User:administrator successfully logged in 2021-05-23 22:22:36,324 DEBUG [1] ModuleController - Starting 2021-05-23 22:22:36,440 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options on parent! 2021-05-23 22:22:36,786 DEBUG [1] FragmentMatchConfigPresenter1 - Showing fragment match chart options docked! 2021-05-23 22:22:40,686 DEBUG [1] ServerAccessService - User: Administrator attempts to login at server: localhost 2021-05-23 22:22:41,721 INFO [8] ModuleController - Preparing Study Loading took 2 ms. 2021-05-23 22:22:42,154 INFO [1] ModuleController - Show start page 2021-05-23 22:23:53,605 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 1. Available Memory: 26345/32767 MB 2021-05-23 22:23:54,651 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:54,684 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:55,163 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:55,252 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:23:55,268 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 14 ms 2021-05-23 22:23:55,283 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:55,305 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1687 ms 2021-05-23 22:23:56,285 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:23:56,295 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:23:56,315 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:23:56,327 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:23:56,349 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:23:56,376 ERROR [1] StudyManagerWorkItemController - Create new study failed: Could not find a part of the path. System.IO.DirectoryNotFoundException: Could not find a part of the path. at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath) at System.IO.File.InternalMove(String sourceFileName, String destFileName, Boolean checkHost) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.PersistStudyToXmlFile(String fileName, Boolean createBackup, CancellationToken token) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.SaveStudyToFile(String fileName) at

Thermo.Discoverer.StudyManagement.Controls.Models.StudyManagementViewModel.CreateNewStudy(String studyFileName, String studiesDirectory, String studyTemplateFileName, QuanMethod quanMethod, Boolean remote) at

Thermo.Discoverer.WorkflowEditorModule.StudyManagerWorkItemController.d__56.MoveNext() 2021-05-23 22:23:58,557 ERROR [1] WindowsFormsMessageService - Message: Create new study failed: Could not find a part of the path.; Result: OK 2021-05-23 22:25:08,170 DEBUG [1] StudyManagerWorkItemController - Open studies (after open): 2. Available Memory: 26268/32767 MB 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:09,223 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:09,253 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:09,282 INFO [1] WorkflowEditorStudyViewExtensionPart - Creating study extension part of type WorkflowEditorStudyViewExtensionPart... 2021-05-23 22:25:09,282 DEBUG [1] WorkflowEditorStudyViewExtensionPart - Initializing WorkflowEditorView took 2 ms 2021-05-23 22:25:09,286 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:09,326 INFO [1] StudyManagerWorkItemController - Initializing Study Management took 1153 ms 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: StudyDefinitionEditorView 2021-05-23 22:25:10,270 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleFileCentricView 2021-05-23 22:25:10,337 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: SampleCentricView 2021-05-23 22:25:10,356 INFO [1] StudyDefinitionDependentStudyViewExtensionPart1 - Creating content for study extension part of type: QuantificationStudyView 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:25:10,373 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:10,391 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:25:34,691 DEBUG [1] StudyManagementViewModel - Auto save timer started. 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:25:50,805 DEBUG [1] WorkflowTree - Validation of processing node "Sequest HT(3)" failed. Missing value for parameter 'Protein Database' 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:27:34,692 DEBUG [16] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:29:34,725 DEBUG [10] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:31:34,739 DEBUG [9] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:33:34,756 DEBUG [26] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Requesting new exclusive token source 2021-05-23 22:35:34,774 DEBUG [27] StudyManagementViewModel - Creating new exclusive token source 2021-05-23 22:37:16,229 INFO [1] DataSequenceStarter - Start submitting of 1 analysis sequences... 2021-05-23 22:37:16,350 INFO [17] DataSequenceStarter - Found 0 of 3 files on the server. 2021-05-23 22:37:19,027 INFO [6] DataSequenceStarter - Found 1 of 1 files on the server. 2021-05-23 22:37:19,764 INFO [1] DataSequenceStarter - Submitting analysis sequence took 3534 ms (Workflow: TargetedDiscovery, Result Filename: E:\5kProteinProject_20210512\20210515\studies\RC5 30min PharmaF

Baseline\TESTING_202100523_RC5_30min-PharmaF_50cm_TE-DDA-Baseline.pdResult). 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Requesting new exclusive token source 2021-05-23 22:37:19,791 DEBUG [1] StudyManagementViewModel - [ASYNC] Creating new exclusive token source 2021-05-23 22:37:19,882 DEBUG [1] StudyManagementViewModel - Auto save timer stopped. 2021-05-23 22:37:19,911 DEBUG [1] AdminViewWorkItemController - Starting 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Setting directories: Current directory '', new directory '' 2021-05-23 22:37:20,620 DEBUG [1] DiscovererDaemonConfigurationViewPresenter - Directories were set: Current directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, new directory C:\ProgramData\Thermo\Proteome Discoverer 2.4\PublicFiles, enabled True 2021-05-23 22:37:20,773 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same display name defined twice 'Completed' 2021-05-23 22:37:21,932 WARN [1] EnumHelper - The enum of type Thermo.Magellan.BL.Data.ExecutionState has the same abbreviation defined twice 'Completed' 2021-05-23 23:13:07,871 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory , enabled True 2021-05-23 23:13:42,030 INFO [1] WindowsFormsMessageService - Message: You changed the file directory to E:\Scratch. The change will be applied when Proteome Discoverer starts next time. Do you want to save the changes?; Result: Yes 2021-05-23 23:13:42,339 DEBUG [1] TempFolderViewPresenter - Directories were set: Current directory D:\Scratch, new directory E:\Scratch, enabled True 2021-05-23 23:13:48,296 INFO [1] ShellApplication - Closing shell. 2021-05-23 23:13:48,438 INFO [1] ShellApplication - Request server shut down. 2021-05-23 23:13:49,151 DEBUG [1] ShellApplication - Closing server took 711 ms 2021-05-23 23:13:49,348 DEBUG [1] AdminViewWorkItemController - Terminating 2021-05-23 23:13:49,462 DEBUG [1] StudyManagerWorkItemController - Open studies (after close): 1. Available Memory: 26220/32767 MB 2021-05-23 23:13:49,615 DEBUG [1] ShellApplication - Close server from Main

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

Nesvilab / PD-Nodes

PD 2.4 Node installation error #20