Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/672b25c503968c5896c13d77881d7b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/672b25c503968c5896c13d77881d7b/.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/cb/500e3118c079b5854616acae63ac32/659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 122
  Pass (FILTER=PASS): 10 (8.2%)
  Fail (FILTER=FAIL): 112 (91.8%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 21
  confidence_below_min(medium<high): 17
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 3
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 2

Breakdown by confidence:
  high: 10 pass, 4 fail (total: 14)
  low: 0 pass, 44 fail (total: 44)
  medium: 0 pass, 64 fail (total: 64)
Arriba filter: 122 rows -> 10 PASS; wrote 659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_dts-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt