MQ2.4.2.0 DIA vs .wiff files crash

[tretyacv]

Describe the bug Running any MaxDIA pipeline using .wiff as input fails on Feature detection step:

Configuring
Assemble run info
Finish run info
Testing fasta files
Preparing searches
Generate libraries
Feature detection

Unhandled Exception: System.Exception: Exception during execution of external process: 12508 Unhandled exception. System.IO.FileNotFoundException: Could not find file 'C:\Users\slavat.WISMAIN\Dow       nloads\T8_kin_1_\p0\T8_kin_1_.bg.dia0'.
File name: 'C:\Users\slavat.WISMAIN\Downloads\T8_kin_1_\p0\T8_kin_1_.bg.dia0'
   at System.IO.FileStream.ValidateFileHandle(SafeFileHandle fileHandle)
   at System.IO.FileStream.CreateFileOpenHandle(FileMode mode, FileShare share, FileOptions options)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share, Int32 bufferSize, FileOptions options)
   at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
   at BaseLibS.Util.FileUtils.GetBinaryReader(String path)
   at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.DetectFeatures(MaxQuantParams mqpar, Int32 taskIndex, Boolean positiveMode, Responder responder, Int32 batchBegin, Int32 batchEnd       )
   at MaxQuantLibS.Domains.Peptides.Features.FeatureDetectionUtil.DetectFeatures(String mqparFile, Int32 taskIndex, Boolean positiveMode, Responder responder, Int32 batchBegin, Int32 batchEnd)
   at MaxQuantLibS.Domains.Peptides.Work.FeatureDetection.Calculation(String[] args, Responder responder)
   at MaxQuantLibS.Domains.Peptides.Work.MaxQuantWorkDispatcherUtil.PerformTask(Int32 taskType, String[] args, Responder responder)
   at MaxQuantLibS.Base.MaxQuantUtils.Run(Int32 softwareId, Int32 taskType, String[] args, Responder responder)
   at MaxQuantTaskCore.Program.Function(String[] args, Responder responder)
   at Utils.Util.ExternalProcess.Run(String[] args, Boolean debug)
   at MaxQuantTaskCore.Program.Main(String[] args)

   at QueueingSystem.WorkDispatcher.ProcessSingleRunExternalProcess(Int32 taskIndex, Int32 threadIndex)
   at QueueingSystem.WorkDispatcher.DoWork(Int32 taskIndex, Int32 threadIndex)
   at QueueingSystem.WorkDispatcher.Work(Object threadIndex)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Threading.ThreadHelper.ThreadStart(Object obj)

Same error happens in GUI

To Reproduce Steps to reproduce the behavior:

1. Go to 'any DIA dataset in .wiff format https://www.ebi.ac.uk/pride/archive/projects/PXD036444'
2. Click on 'run MaxDIA in discovery mode with fasta/evidence/msms files from MQ web'
3. See error

Expected behavior Not crashing, this does not happen when .raw files are used as input

Screenshots If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows
• Version 10

Additional context Add any other context about the problem here.

[tretyacv]

the issue also reported here - https://groups.google.com/g/andromeda-list/c/FgmIHqVAvPQ

[dtabb73]

I had the same experience with the feature detector in MaxQuant 2.5.0.0 using WIFF files from PXD002965, though the error was "could not find file". I should add that I successfully produced my spectral library in MaxQuant from DDA WIFFs in this PXD. This "could not find file" failure occurred when attempting to use MaxDIA to quantify in DIA WIFFs on the basis of the spectral library the software reported to the spectral library in the first step.

[zznx]

Is it the same problem? Is it solved yet? (wiff and IDA)

[dtabb73]

Have you tried with version 2.6.2.0? I have not updated from 2.5.0.0, but I was unable to get MaxDIA in MaxQuant 2.5.0.0 to read WIFFs from either of two IDA ProteomeXchange projects.

[zznx]

I used MaxQuant_v2.6.1.0, but it didn't work.

[wangss3]

Same issue with wiff files (version 2.6.5.0).

But my orbitrap raw data worked fine.