Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/91e9e49f0cf9fb522db833a2c70f21/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/91e9e49f0cf9fb522db833a2c70f21/.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/96/ae7a70ecabdef6a125a1c880a6abe0/aih-tih-sc-099ac4-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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 307
  Pass (FILTER=PASS): 29 (9.4%)
  Fail (FILTER=FAIL): 278 (90.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 61
  confidence_below_min(low<high): 49
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 42
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<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(6.0<8.0): 3
  confidence_below_min(low<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 29 pass, 6 fail (total: 35)
  low: 0 pass, 169 fail (total: 169)
  medium: 0 pass, 103 fail (total: 103)
Arriba filter: 307 rows -> 29 PASS; wrote aih-tih-sc-099ac4-R1_B23WHYVLT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-099ac4-R1_B23WHYVLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-099ac4-R1_B23WHYVLT4_1.arriba.fusions.filter_summary.txt