Error exit status (139)

[thanadol-git]

Hi,

I am running several quantms runs recently to test one of our DIA experiments. I just got the message below without any suggestion. I am not sure where to check, but I guess the two files might be corrupted. Have you ever seen this error messages?

[-        ] BIG…D:PSM_RESCORING:PERCOLATOR -
[dd/bc2e4f] BIG… (scapis_dia.plate12.sdrf) | 1 of 1, cached: 1 ✔
[bf/f691af] BIG…ION (human_proteome.fasta) | 1 of 1, cached: 1 ✔
[00/945222] BIG… (20250715_Scapis_P12_G12) | 94 of 96, cached: 94, retries: 2
Plus 7 more processes waiting for tasks…
-[bigbio/quantms] Pipeline completed with errors-
[65/f36d4b] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS (20250715_Scapis_P12_H11)` terminated with an error exit status (139) -- Execution is retried (1)
[49/3a2666] NOTE: Process `BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS (20250715_Scapis_P12_G12)` terminated with an error exit status (139) -- Execution is retried (1)
WARN: Killing running tasks (1)
ERROR ~ Error executing process > 'BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS (20250715_Scapis_P12_H11)'

Caused by:
  Process `BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS (20250715_Scapis_P12_H11)` terminated with an error exit status (139)


Command executed:

  # Precursor Tolerance value was: 10.0
  # Fragment Tolerance value was: 0.05
  # Precursor Tolerance unit was: ppm
  # Fragment Tolerance unit was: Da
  
  # Final mass accuracy is ''
  
  diann   --lib lib.predicted.speclib \
          --f 20250715_Scapis_P12_H11.mzML \
          --threads 24 \
          --verbose 3 \
           \
          --temp ./ \
           \
          --quick-mass-acc --min-corr 2 --corr-diff 1 --time-corr-only
  
  cp report.log.txt 20250715_Scapis_P12_H11_diann.log
  
  cat <<-END_VERSIONS > versions.yml
  "BIGBIO_QUANTMS:QUANTMS:DIA:PRELIMINARY_ANALYSIS":
      DIA-NN: $(diann 2>&1 | grep "DIA-NN" | grep -oP "\d+\.\d+(\.\w+)*(\.[\d]+)?")
  END_VERSIONS

Command exit status:
  139

Command output:
  DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
  Compiled on Apr 15 2022 08:45:18
  Current date and time: Tue Jan 27 22:22:14 2026
  Logical CPU cores: 32
  Thread number set to 24
  A fast algorithm will be used to select the MS2 mass accuracy setting
  Only peaks with correlation sum exceeding 2 will be considered
  Peaks with correlation sum below 1 from maximum will not be considered
  A single score will be used until RT alignment to save memory; this can potentially lead to slower search
  DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
  
  1 files will be processed
  [0:00] Loading spectral library lib.predicted.speclib
  [0:04] Library annotated with sequence database(s): human_proteome.fasta
  [0:04] Gene names missing for some isoforms
  [0:04] Library contains 20393 proteins, and 20192 genes
  [0:06] Spectral library loaded: 20393 protein isoforms, 29255 protein groups and 5490291 precursors in 2249526 elution groups.
  [0:06] Initialising library
  
  [0:11] File #1/1
  [0:11] Loading run 20250715_Scapis_P12_H11.mzML

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  WARNING: Not virtualizing pid namespace by configuration
  DIA-NN 1.8.1 (Data-Independent Acquisition by Neural Networks)
  Compiled on Apr 15 2022 08:45:18
  Current date and time: Tue Jan 27 22:22:14 2026
  Logical CPU cores: 32
  Thread number set to 24
  A fast algorithm will be used to select the MS2 mass accuracy setting
  Only peaks with correlation sum exceeding 2 will be considered
  Peaks with correlation sum below 1 from maximum will not be considered
  A single score will be used until RT alignment to save memory; this can potentially lead to slower search
  DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme.
  
  1 files will be processed
  [0:00] Loading spectral library lib.predicted.speclib
  [0:04] Library annotated with sequence database(s): human_proteome.fasta
  [0:04] Gene names missing for some isoforms
  [0:04] Library contains 20393 proteins, and 20192 genes
  [0:06] Spectral library loaded: 20393 protein isoforms, 29255 protein groups and 5490291 precursors in 2249526 elution groups.
  [0:06] Initialising library
  
  [0:11] File #1/1
  [0:11] Loading run 20250715_Scapis_P12_H11.mzML
  .command.sh: line 16: 137443 Segmentation fault      diann --lib lib.predicted.speclib --f 20250715_Scapis_P12_H11.mzML --threads 24 --verbose 3 --temp ./ --quick-mass-acc --min-corr 2 --corr-diff 1 --time-corr-only

Work dir:
  /proj/naiss2024-6-415/users/x_thasu/Github/pridepy/load/scapis/P12/work/a8/479317545757dafe342d5c472e4376

Container:
  /proj/naiss2024-6-415/users/x_thasu/Github/pridepy/load/scapis/P12/work/singularity/containers.biocontainers.pro-s3-SingImgsRepo-diann-v1.8.1_cv1-diann_v1.8.1_cv1.img.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details

[jpfeuffer]

Hmm this is probably a DIANN "bug". But since it happens during loading of the mzml it might indeed be triggered by a corrupted mzml. But probably DIANN should fail nicer if this is the case (as you said, segmentation faults do not say much).
You can try to load the file in another program like OpenMS FileInfo or a python library to see if they can handle it.

[thanadol-git]

@jpfeuffer Thanks a lot for that.

I have checked the two files with OpenMS FileInfo and also opened them a bit with TOPPView. I would say they both look very nice for DIA relatively to other injections in the same experiment. Anyway, what would you recommend to check the raw/mzML files after injection?

Million thanks,
Thanadol