Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/7871574d06854b6d8e2b4de77fa767/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/5f1920932e5819b77609d78b612eb6/659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/7871574d06854b6d8e2b4de77fa767/.command.run
  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: 96
  Pass (FILTER=PASS): 5 (5.2%)
  Fail (FILTER=FAIL): 91 (94.8%)

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(5.0<8.0): 20
  confidence_below_min(medium<high): 14
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(low<high): 1

Breakdown by confidence:
  high: 5 pass, 2 fail (total: 7)
  low: 0 pass, 31 fail (total: 31)
  medium: 0 pass, 58 fail (total: 58)
Arriba filter: 96 rows -> 5 PASS; wrote 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt