Error executing process > 'TEST_STARFUSION_FILTER_V2_WORKFLOW:STARFUSION_FILTER (659_cX2_T1_TRNA_1_B2372Y3LT4_1)'

Caused by:
  Process `TEST_STARFUSION_FILTER_V2_WORKFLOW:STARFUSION_FILTER (659_cX2_T1_TRNA_1_B2372Y3LT4_1)` terminated with an error exit status (1)


Command executed:

  echo "=== DEBUGGING INFORMATION ==="
  echo "Current working directory: $(pwd)"
  echo "Input files:"
  echo "  - starfusion_tsv: 659_cX2_T1_TRNA_1_B2372Y3LT4_1.rnafusions.aih.tsv"
  echo "  - blacklist: blacklist_hg38_GRCh38_v2.4.0.tsv.gz"
  echo "  - filter_config: starfusion_filter_config.yaml"
  echo "  - aih_blacklist_breakpoints: blacklist_breakpoint_database_2026-04-27.tsv"
  
  echo ""
  echo "=== PYTHON INFORMATION ==="
  which python || echo "python not found in PATH"
  python --version || echo "python --version failed"
  which python3 || echo "python3 not found in PATH"
  python3 --version || echo "python3 --version failed"
  
  echo ""
  echo "=== SCRIPT LOCATION ==="
  echo "Checking for filter_starfusion_main.py:"
  which filter_starfusion_main.py || echo "filter_starfusion_main.py not found in PATH"
  ls -la filter_starfusion_main.py 2>/dev/null || echo "filter_starfusion_main.py not in current directory"
  ls -la bin/filter_starfusion_main.py 2>/dev/null || echo "bin/filter_starfusion_main.py not found"
  if [ -d bin ]; then
      echo "bin/ directory exists:"
      ls -la bin/ || echo "Could not list bin/ directory"
  else
      echo "bin/ directory does not exist"
  fi
  
  echo ""
  echo "=== ENVIRONMENT PATH ==="
  echo $PATH
  
  echo ""
  echo "=== CURRENT DIRECTORY CONTENTS ==="
  ls -la
  
  echo ""
  echo "=== PROJECT DIRECTORY INFO ==="
  echo "NXF_PROJECT_DIR: ${NXF_PROJECT_DIR:-not set}"
  echo "baseDir: ${baseDir:-not set}"
  
  echo ""
  echo "=== Running filter script ==="
  AIH_TS="${PWD}/_empty_aih_blacklist.tsv"
  if [[ -n 'blacklist_breakpoint_database_2026-04-27.tsv' ]] && [[ -f 'blacklist_breakpoint_database_2026-04-27.tsv' ]]; then
      AIH_TS='blacklist_breakpoint_database_2026-04-27.tsv'
  else
      printf 'BREAKPOINT_ID\tblacklist_evidence_score\n' > "$AIH_TS"
  fi
  filter_starfusion_main.py \
      --input 659_cX2_T1_TRNA_1_B2372Y3LT4_1.rnafusions.aih.tsv \
      --blacklist blacklist_hg38_GRCh38_v2.4.0.tsv.gz \
      --aih-blacklist-breakpoints "$AIH_TS" \
      --filter-config starfusion_filter_config.yaml \
      --output 659_cX2_T1_TRNA_1_B2372Y3LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv \
      --summary 659_cX2_T1_TRNA_1_B2372Y3LT4_1.starfusion.starfusion.fusion_predictions.filter_summary.txt \
      --add-reason-column \
  
  
  # The script creates pass_only file by replacing .tsv with _pass_only.tsv
  # Python: args.output.replace('.tsv', '_pass_only.tsv')
  # So: 659_cX2_T1_TRNA_1_B2372Y3LT4_1.starfusion.starfusion.fusion_predictions.filtered.tsv -> 659_cX2_T1_TRNA_1_B2372Y3LT4_1.starfusion.starfusion.fusion_predictions.filtered_pass_only.tsv
  # No rename needed - script already creates it with correct name
  
  cat <<-END_VERSIONS > versions.yml
  "TEST_STARFUSION_FILTER_V2_WORKFLOW:STARFUSION_FILTER":
      filter_starfusion_main.py: "1.0"
      pandas: $(python -c "import pandas; print(pandas.__version__)" 2>/dev/null || echo "unknown")
      numpy: $(python -c "import numpy; print(numpy.__version__)" 2>/dev/null || echo "unknown")
      pyyaml: $(python -c "import yaml; print(yaml.__version__)" 2>/dev/null || echo "unknown")
      boto3: $(python -c "import boto3; print(boto3.__version__)" 2>/dev/null || echo "unknown")
  END_VERSIONS

Command exit status:
  1

Command output:
    - blacklist: blacklist_hg38_GRCh38_v2.4.0.tsv.gz
    - filter_config: starfusion_filter_config.yaml
    - aih_blacklist_breakpoints: blacklist_breakpoint_database_2026-04-27.tsv
  
  === PYTHON INFORMATION ===
  /usr/local/bin/python
  Python 3.11.14
  /usr/local/bin/python3
  Python 3.11.14
  
  === SCRIPT LOCATION ===
  Checking for filter_starfusion_main.py:
  /tmp/nxf.ADxZ0TgDtV/nextflow-bin/filter_starfusion_main.py
  filter_starfusion_main.py not in current directory
  bin/filter_starfusion_main.py not found
  bin/ directory does not exist
  
  === ENVIRONMENT PATH ===
  /tmp/nxf.ADxZ0TgDtV/nextflow-bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
  
  === CURRENT DIRECTORY CONTENTS ===
  total 64244
  drwx------. 3 1000 root     4096 Jun  5 22:47 .
  drwxrwxrwx. 5 root root      101 Jun  5 22:47 ..
  -rw-r--r--. 1 1000 root        0 Jun  5 22:47 .command.err
  -rw-r--r--. 1 1000 root      855 Jun  5 22:47 .command.out
  -rw-r--r--. 1 1000 root    15891 Jun  5 22:47 .command.run
  -rw-r--r--. 1 1000 root     3154 Jun  5 22:47 .command.sh
  -rw-r--r--. 1 1000 root        0 Jun  5 22:47 .command.trace
  -rw-r--r--. 1 1000 root   247066 Jun  5 22:47 659_cX2_T1_TRNA_1_B2372Y3LT4_1.rnafusions.aih.tsv
  -rw-r--r--. 1 1000 root 10714998 Jun  5 22:47 blacklist_breakpoint_database_2026-04-27.tsv
  -rw-r--r--. 1 1000 root 54779787 Jun  5 22:47 blacklist_hg38_GRCh38_v2.4.0.tsv.gz
  drwxr-xr-x. 4 1000 root     4096 Jun  5 22:47 nextflow-bin
  -rw-r--r--. 1 1000 root     4132 Jun  5 22:47 starfusion_filter_config.yaml
  
  === PROJECT DIRECTORY INFO ===
  NXF_PROJECT_DIR: not set
  baseDir: not set
  
  === Running filter script ===
  
  ================================================================================
  STEP 1: LOADING STAR-FUSION PREDICTIONS
  ================================================================================
  Loading STAR-Fusion predictions from: 659_cX2_T1_TRNA_1_B2372Y3LT4_1.rnafusions.aih.tsv
    ✓ Loaded: 870 fusions
  
  ================================================================================
  STEP 2: CONVERTING TO BREAKPOINT_ID FORMAT
  ================================================================================

Command error:
  ✗ Error converting format: 'LeftBreakpoint'

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/a045cc6dd6f1ac20e3a8ff49f11282

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/fusion-filter:ccc640033dca

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