Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/a85d11ecc171eae0a18f9f4a23b962/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/a85d11ecc171eae0a18f9f4a23b962/.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/c4/575fb4624a9a091ba2d003769659f6/aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 242
  Pass (FILTER=PASS): 16 (6.6%)
  Fail (FILTER=FAIL): 226 (93.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 76
  confidence_below_min(low<high): 22
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<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(7.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 16 pass, 4 fail (total: 20)
  low: 0 pass, 92 fail (total: 92)
  medium: 0 pass, 130 fail (total: 130)
Arriba filter: 242 rows -> 16 PASS; wrote aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-c9a01b-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt