Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/93f14a87360d072a60db59d5176d62/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/93f14a87360d072a60db59d5176d62/.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/36/54f68928f92e114ae7d0651fdb041f/aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-5ae5f7b1-ce8a-4a12-9374-820c751df9c5/09/a7ecdb27117590dd6e7bf9e221420e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 333
  Pass (FILTER=PASS): 42 (12.6%)
  Fail (FILTER=FAIL): 291 (87.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 101
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(low<high): 13
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 42 pass, 8 fail (total: 50)
  low: 0 pass, 109 fail (total: 109)
  medium: 0 pass, 174 fail (total: 174)
Arriba filter: 333 rows -> 42 PASS; wrote aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-4ca6a8-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt