search

Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
8 stars 1 forks source link

"FileNotFoundException" Issue Running MSFragger on PD 3.0 #40

Open sschlange opened 2 weeks ago

sschlange commented 2 weeks ago

Hello,

I am having an error interrupt PD searches when running the MSFragger Node on PD 3.0. MSFragger version 4.1. It seems MSFragger is unsuccessful in generating the pepXML files in the temp folder. I am working with 25 GB RAM.

I do believe this is a similar issue as discussed here (https://github.com/Nesvilab/PD-Nodes/issues/1), but I cannot resolve it so far.

20241002_PD Error fragger_closed.zip

huiyinc commented 2 weeks ago

Hi,

Could you please send me the log file reported by PD, so I can take a look of the issue? Thanks.

Huiyin

sschlange @.***> 於 2024年10月3日 上午2:27 寫道：



Hello,

I am having an error interrupt PD searches when running the MSFragger Node on PD 3.0. MSFragger version 4.1. It seems MSFragger is unsuccessful in generating the pepXML files in the temp folder. I am working with 25 GB RAM.

I do believe this is a similar issue as discussed here (#1 https://github.com/Nesvilab/PD-Nodes/issues/1), but I cannot resolve it so far.

20241002_PD.Error.PNG (view on web) https://github.com/user-attachments/assets/5a3332d0-01ea-4077-8227-8b10617e24b8 fragger_closed.zip https://github.com/user-attachments/files/17234437/fragger_closed.zip

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/40, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA5PWSOM2P66NWKFA7DZZQ3JNAVCNFSM6AAAAABPIHOJZOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3DEMZYGA4DONI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

sschlange commented 2 weeks ago

In C:\ProgramData\Thermo\Proteome Discoverer 3.0\Logs I do not have any file called MagellanServer.log. Here is a zip of my Logs folder

Logs.zip

huiyinc commented 1 week ago

Hi,

I checked the log file, and there is an error message in the log file (Discoverer.log.25). It seems that you install MSFraggerPDv25.dll in PD v3.0. The version is inconsistent. Please install MSFraggerPDv30.dll, instead. If you install MSFraggerPDv30.dll, but still get errors, please feel free to let me know. Thanks.

Huiyin

2024-09-30 14:49:40,902 WARN [1] LicenseManager - Could not load this assembly "MSFraggerPDv25.dll" since the following exception is raised System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Program Files\Thermo\Proteome Discoverer 3.0\Proteome Discoverer 3.0\System\Release\MSFraggerPDv25.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Program Files\Thermo\Proteome Discoverer 3.0\Proteome Discoverer 3.0\System\Release\MSFraggerPDv25.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.FT()

sschlange @.***> 於 2024年10月3日 下午11:06 寫道：



In C:\ProgramData\Thermo\Proteome Discoverer 3.0\Logs I do not have any file called MagellanServer.log. Here is a zip of my Logs folder

Logs.zip https://github.com/user-attachments/files/17246220/Logs.zip

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/40#issuecomment-2391662540, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA2I5YTAIO3IQWE2TZ3ZZVMOBAVCNFSM6AAAAABPIHOJZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJRGY3DENJUGA . You are receiving this because you commented.Message ID: @.***>

sschlange commented 1 week ago

Hello,

I have installed MSFraggerPDv30.dll on 9/30 as pictured. image

Still, I tried again and had the same error, pictured below. image

Logs: Logs.zip

Thank you.

huiyinc commented 1 week ago

Hi,

I checked the log file (Discoverer.log.2) and noticed an error message (as attached below). I guess maybe the error is caused by the inconsistency of .NET Framework. The MSFraggerPDv30 is compiled based on .NET Framework 4.7.2. What is the .NET Framework installed in your computer?

Huiyin

2024-10-04 09:17:23,528 WARN [1] SafeDirectoryCatalog - Unable to load one or more of the requested types from the assembly MSFraggerPDv30.dll. Reason: Could not load file or assembly 'MSFraggerPDv30, 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 'MSFraggerPDv30, Version=1.0.0.0, Culture=neutral, PublicKeyToken=null' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'MSFraggerPDv30, 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)

sschlange @.***> 於 2024年10月5日 上午12:49 寫道：



Hello,

I have installed MSFraggerPDv30.dll on 9/30 as pictured. image.png (view on web) https://github.com/user-attachments/assets/0ef64483-af10-4772-a5fe-ffc65173bf0f

Still, I tried again and had the same error, pictured below. image.png (view on web) https://github.com/user-attachments/assets/211826ed-8c47-4d3c-9574-ebe7391e66cc

Logs: Logs.zip https://github.com/user-attachments/files/17261639/Logs.zip

Thank you.

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/40#issuecomment-2394102235, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA3BJFMETWZVWGXGKMTZZ3BIXAVCNFSM6AAAAABPIHOJZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJUGEYDEMRTGU . You are receiving this because you commented.Message ID: @.***>

sschlange commented 1 week ago

image

huiyinc commented 1 week ago

Hi,

Maybe you can install .NET Framework 4.7.2 and see if it solves the problem?

Best,

Huiyin

sschlange @.***> 於 2024年10月8日 上午12:17 寫道：



image.png (view on web) https://github.com/user-attachments/assets/4c276635-9f5f-4ce5-90b6-20bcb5a2d5bb

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/40#issuecomment-2397363766, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAZUTNSU6O5TTWHKCXLZ2KX2XAVCNFSM6AAAAABPIHOJZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJXGM3DGNZWGY . You are receiving this because you commented.Message ID: @.***>

sschlange commented 1 week ago

Hello,

I have tried to download and install .NET framework 4.7.2, but the error message I get from the install indicates that ".NET Framework 4.7.2 or a later update is already installed on this computer." Should I uninstall the newer version to then install NET framework 4.7.2?

huiyinc commented 1 week ago

Hi,

Yes, please try it and let me know if it works. Thanks.

Huiyin

sschlange @.***> 於 2024年10月9日 上午12:05 寫道：



Hello,

I have tried to download and install .NET framework 4.7.2, but the error message I get from the install indicates that ".NET Framework 4.7.2 or a later update is already installed on this computer." Should I uninstall the newer version to then install NET framework 4.7.2?

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/40#issuecomment-2400251670, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAZNMM6PM6BPSW55EBLZ2P7DNAVCNFSM6AAAAABPIHOJZOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBQGI2TCNRXGA . You are receiving this because you commented.Message ID: @.***>