Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/0d9dd0cab367719b5505f3a0dcd443/659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/eff397800cad18adf1ab4f1e249d84/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/eff397800cad18adf1ab4f1e249d84/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 34
  Pass (FILTER=PASS): 11 (32.4%)
  Fail (FILTER=FAIL): 23 (67.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 3
  All 3 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 11 pass, 2 fail (total: 13)
  low: 0 pass, 5 fail (total: 5)
  medium: 0 pass, 16 fail (total: 16)
Arriba filter: 34 rows -> 11 PASS; wrote 659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_dm4-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt