Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/ab651649a35713b0d79e3674fe9cd2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/ab651649a35713b0d79e3674fe9cd2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/28dc27dd0656bb8ad6ef0fa72ad7ab/aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.tsv
  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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 13 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 266
  Pass (FILTER=PASS): 40 (15.0%)
  Fail (FILTER=FAIL): 226 (85.0%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 13
  All 13 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 75
  confidence_below_min(low<high): 33
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 40 pass, 3 fail (total: 43)
  low: 0 pass, 118 fail (total: 118)
  medium: 0 pass, 105 fail (total: 105)
Arriba filter: 266 rows -> 40 PASS; wrote aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-63b0e7-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt