Nextflow workflow report

[cheesy_jones]

Error executing process > 'export_mona (1)'

Caused by:
  Process `export_mona (1)` terminated with an error exit status (4)


Command executed:

  wget -qO- "https://mona.fiehnlab.ucdavis.edu/rest/downloads/retrieve/4ebf9d78-f0d4-470c-b8cb-afc5f6241584" | funzip > "MONA_ML_Export.msp"
  
  mkdir -p "./temp/"
  
  python3 /app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing/bin/MSP_ingest.py           --msp_path "MONA_ML_Export.msp"           --summary_output_path "./temp/MONA-Export.csv"           --spectra_output_path "./temp/MONA-Export.mgf"

Command exit status:
  4

Command output:
  (empty)

Command error:
  funzip error: invalid compressed data--length error

Work dir:
  /data/gscratch/web-services/Cleaning_Pipelines/work/76/e4ebe8a29d076f470973b3a1d31bab

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Run times

02-Oct-2026 09:38:30 - 02-Oct-2026 09:41:33 (duration: 3m 3s)

  2 succeeded  

  0 cached  

  0 ignored  

  1 failed  

Nextflow command

nextflow run /app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing/nf_workflow.nf --GNPS_json_path /output/ALL_GNPS_NO_PROPOGATED.json --output_dir /output/cleaned_data/ --conda_path /app/pipelines/conda_envs/gnps2_ml_processing_env --matchms_conda_path /app/pipelines/conda_envs/matchms_env --api_cache /output/structure_classification/ -with-report /output/cleaned_data/ml_pipeline_report.html -with-timeline /output/cleaned_data/ml_pipeline_timeline.html -w /data/gscratch/web-services/Cleaning_Pipelines/work

CPU-Hours

0.1 (46.3% failed)

Launch directory

/app

Work directory

/data/gscratch/web-services/Cleaning_Pipelines/work

Project directory

/app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing

Script name

nf_workflow.nf

Script ID

d07e4bbd5164ef48fc8bd5c492e8eef2

Workflow session

b83ca6d3-2b4f-433a-9e36-8c1ccfe14126

Workflow profile

standard

Nextflow version

version 24.04.4, build 5917 (01-08-2024 07:05 UTC)