Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/082dfe12f6e02c4dca52249ad103dc/aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/ae40cff428b4d5ff5f95735b0fc0ef/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/ae40cff428b4d5ff5f95735b0fc0ef/.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-8900cb43-4dca-49ac-a290-1d176a2e0012/49/8453bafeca2d0250d89cdefd7ba73e/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: 31
  Pass (FILTER=PASS): 2 (6.5%)
  Fail (FILTER=FAIL): 29 (93.5%)

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

Failure reasons (top 15):
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high): 4
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
  confidence_below_min(medium<high);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 1

Breakdown by confidence:
  high: 2 pass, 0 fail (total: 2)
  low: 0 pass, 21 fail (total: 21)
  medium: 0 pass, 8 fail (total: 8)
Arriba filter: 31 rows -> 2 PASS; wrote aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-89cc59-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt