Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/4d6b2a7f9f81ac1e838227b831804c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/4d6b2a7f9f81ac1e838227b831804c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/ae86ddd00d526b19c349caa0a7d7d5/aih-tih-sc-55b175-R1_A23WJ53LT4_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-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: 213
  Pass (FILTER=PASS): 11 (5.2%)
  Fail (FILTER=FAIL): 202 (94.8%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 28
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 18
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 11 pass, 5 fail (total: 16)
  low: 0 pass, 116 fail (total: 116)
  medium: 0 pass, 81 fail (total: 81)
Arriba filter: 213 rows -> 11 PASS; wrote aih-tih-sc-55b175-R1_A23WJ53LT4_1.arriba.fusions.filtered.tsv and aih-tih-sc-55b175-R1_A23WJ53LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: aih-tih-sc-55b175-R1_A23WJ53LT4_1.arriba.fusions.filter_summary.txt