Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/d26c8da5d5b71d3324a10d39938b3f/659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/cbf31c77e34a47600d13338bbb914d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/cbf31c77e34a47600d13338bbb914d/.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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 192
  Pass (FILTER=PASS): 26 (13.5%)
  Fail (FILTER=FAIL): 166 (86.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 30
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 26 pass, 4 fail (total: 30)
  low: 0 pass, 78 fail (total: 78)
  medium: 0 pass, 84 fail (total: 84)
Arriba filter: 192 rows -> 26 PASS; wrote 659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_bTo-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt