Prepare protein assembly error Maxquant

[doanthaodinh]

I am using MaxQuant 2.8.1.0 and having a recurring error at the 'Prepare protein assembly' step, leading to this error:
False_Index was outside the bounds of the array._ at MqUtil.Ms.Utils.PepUtils.GetNonredGroupInds2(String[] proteinIds, String[][] peptideSeq, Boolean splitTaxonomy, String[] taxIds)_ at MqUtil.Ms.Utils.PepUtils.CreateProteinAndPeptideLists2(String[] proteinIds, String[][] peptideSeq, Byte[][] isMut, Boolean splitTaxonomy, TaxonomyRank rank, ProteinSet proteinSet, Responder responder)_

MaxQuant was run on Linux from terminal (dotnet MaxQuantCmd.dll mqpar.xml) on Bruker .d input folder, with mqpar.xml generated from an equivalent Windows version of MaxQuant, and human protein fasta obtained from Uniprot (UP000005640_9606.fasta). The input file has been independently analysed successfully using Spectronaut. The following versions of the protein fasta file have been tested and yielded the same error:

• Removal of entries with duplicated header
• Removal of entries with duplicated sequences
• Removal of selenoprotein entries

Happy to test with a minimal working human protein fasta version.

[WalterViegener]

please upload your mqpar file here

[doanthaodinh]

Hi, couldn't see an upload function on the link provided so I've attached a copy of the mqpar file here.
mqpar.xml

[WalterViegener]

I changed the first link now to a file upload link (sorry for that)
Can you please upload or check the combined/diaProteinIds2 file? is that empty?
Also try to turn diaIncreaseSequenceCoverage=False

if the file is empty and the diaIncreaseSequenceCoverage change does not work please upload that raw file and fasta file you have in your mpar

[s268490t-cpu]

Hi, I'm experiencing what appears to be the same issue with MaxQuant 2.8.1.0, but with a different dataset and instrument, so I wanted to add another independent reproduction case.
Environment

• MaxQuant 2.8.1.0
• Linux: AlmaLinux 10.1
• Thermo Orbitrap Exploris 480
• Standard DDA acquisition
• In-house genome annotation FASTA
  Error
  The analysis proceeds normally through identification, FDR filtering, and match between runs, but consistently fails at:
  Prepare protein assembly
  with:
  Index was outside the bounds of the array.
  and the stack trace includes:
  MqUtil.Ms.Utils.PepUtils.GetNonredGroupInds2(...)
  I have reproduced this with multiple independent datasets, including a dataset that had previously completed successfully.
  I also tested the following without resolving the issue:
• reducing the number of threads to 1
• explicitly setting taxonomyId
• setting diaIncreaseSequenceCoverage=False
• re-downloading MaxQuant 2.8.1.0 (MD5 checksum identical)
• reinstalling the .NET environment
  I initially also encountered the SDRF-related crash, but that was successfully bypassed by pre-creating an empty sdrf.tsv.
  Because this reproduces with Thermo RAW data and non-UniProt FASTA files, it may indicate that the GetNonredGroupInds2 issue is not specific to Bruker data or the original FASTA used in this issue.
  Please let me know if any additional logs, mqpar.xml, or minimal test files would be useful for debugging.