Process 'WriteSubMzml' finished, exit code: 1

[lbwfff]

Dear Developers,

Thanks for the recent update, I'm very excited about two-pass search, but I'm experiencing an error reported when I Write sub mzML.

Here is the message:

Please wait. WriteSubMzml is running. It can take a long time.
Please wait. WriteSubMzml is running. It can take a long time.
Failed to find scan name or probability threshold in /scratch/lb4489/project/MS_data/NBT_pro/fragpipe/test/twostep/trypsin_HCD/psm.tsv
Found /scratch/lb4489/project/MS_data/NBT_pro/trypsin/trypsin_HCD/20151201_alr_CompleteHumanProteome_HepG2_HCD_trypsin_fr2.mzBIN_all.
Failed to find scan name or probability threshold in /scratch/lb4489/project/MS_data/NBT_pro/fragpipe/test/twostep/trypsin_HCD/psm.tsv
Found /scratch/lb4489/project/MS_data/NBT_pro/trypsin/trypsin_HCD/20151201_alr_CompleteHumanProteome_HepG2_HCD_trypsin_fr1.mzBIN_all.
Process 'WriteSubMzml' finished, exit code: 1
Process 'WriteSubMzml' finished, exit code: 1
Process returned non-zero exit code, stopping
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 6 remaining tasks

Here is the full log:
slurm-7833617.txt

How do I fix this?

Thanks,

LeeLee

[fcyu]

Hi LeeLee,

Could you share /scratch/lb4489/project/MS_data/NBT_pro/fragpipe/test/twostep/trypsin_HCD/psm.tsv with us?

Thanks,

Fengchao

[lbwfff]

Hi Fengchao, thanks for your reply. I uploaded the file to dropbox and you should be able to download it through this
link.

[fcyu]

Hi LeeLee,

Thanks for the prompt response. The psm.tsv file looks OK. Then, I have no idea about the error. Could you first run a small dataset on Windows to see if it works well? Not sure if some configurations on you Linux server caused the issue.

Thanks,

Fengchao

[lbwfff]

Hi, Fengchao. tried to analyze one of the fractions on my pc, and at least there is no error in the first-pass search. It seems that the problem occurs only on Linux.

[lbwfff]

Hi, Fengchao.

Are there any plans to address this issue in a future update? I apologize for any extra workload this may cause, but due to the large amount of data, it's challenging to complete the analysis on Windows. It would be incredibly helpful if this could be supported.

Thanks a lot for considering this.

Best,

LeeLee

[fcyu]

Hi LeeLee,

Since it works on your Windows but not your Linux server, it should be something related to your server configuration but not our tool's problem.

Please contact your IT department to troubleshoot it locally.

Best,

Fengchao