Error with demo data in 'mass_spec_raw_convert'

[almart7]

Dear developers,

Thank you for this great tool. I just installed it and tried to run the pipeline with the test_without_sqanti.config but it crashes with the following error:

Error executing process > 'mass_spec_raw_convert'

Caused by:
  Process `mass_spec_raw_convert` terminated with an error exit status (1)

Command executed:

  wine msconvert 120426_Jurkat_highLC_Frac28.raw --filter "peakPicking true 1-"

Command exit status:
  1

Command output:
  (empty)

Command error:
  wine: socket : Function not implemented

Do you have any suggestions on how to solve this?

Kind regards

[Sktbanerjee1]

Thank you for using our pipeline and reaching out with the issue.

• This might be a Wine installation-related problem. Please make sure you can run Wine outside of the LRP.
• This might also be an IP-related issue, as wine uses the Linux API. Running systemctl reload apparmor.service command in your terminal, and restarting the system might fix it.
• It might also be worth checking the iptable on your specific system.

I hope this helps; please feel free to reach out if the problem persists.

[almart7]

Hello again,

Thank you for your response. I was able to solve the problem but I found another one. I have this error message:

Error executing process > 'metamorpheus_with_gencode_database (120426_Jurkat_highLC_Frac28.mzML)'

Caused by:
  Process `metamorpheus_with_gencode_database (120426_Jurkat_highLC_Frac28.mzML)` terminated with an error exit status (1)

Command executed:

  dotnet /metamorpheus/CMD.dll -g -o ./toml --mmsettings ./settings
  dotnet /metamorpheus/CMD.dll -d gencode_protein.fasta settings/Contaminants/MetaMorpheusContaminants.xml -s 120426_Jurkat_highLC_Frac28.mzML -t toml/SearchTask.toml -v normal --mmsettings settings -o ./search_results
  
  mv search_results/Task1SearchTask/AllPeptides.psmtsv search_results/Task1SearchTask/AllPeptides.Gencode.psmtsv
  mv search_results/Task1SearchTask/AllQuantifiedProteinGroups.tsv search_results/Task1SearchTask/AllQuantifiedProteinGroups.Gencode.tsv

Command exit status:
  1

Command output:
  Welcome to MetaMorpheus
  
  CMD 1.0.0
  
  ERROR(S):
    Option 'c' is unknown.