Nextflow workflow report

[focused_lattes]

Error executing process > 'prep_params_massbank'

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


Command executed:

  python3 /app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing/../MassBank_Processing/bin/prep_params.py             --glob "MassBank-data/*/*.txt"             --blacklist "legacy.blacklist"             -p "10000"
  
  # python3 /app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing/../MassBank_Processing/bin/prep_params.py   #         --glob "MassBank-data/MSSJ/*.txt"   #         --blacklist "legacy.blacklist"   #         -p "10000"

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/app/pipelines/gnps_ml_processing_workflow/GNPS_ML_Processing/../MassBank_Processing/bin/prep_params.py", line 5, in 
      import numpy as np
  ModuleNotFoundError: No module named 'numpy'

Work dir:
  /data/gscratch/web-services/Cleaning_Pipelines/work/f0/967fcec718945e7c87ee69d1ae3a90

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

Run times

25-Jan-2026 15:53:24 - 25-Jan-2026 16:01:14 (duration: 7m 50s)

  4 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

0.3 (0.2% 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

c96f067e-2ab1-4361-bf10-6f3bdc226364

Workflow profile

standard

Nextflow version

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