Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/02adf090d2c533862e9d7f1d03850c/tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/5106a9517ba593b060183233db3402/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/5106a9517ba593b060183233db3402/.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: 107
  Pass (FILTER=PASS): 4 (3.7%)
  Fail (FILTER=FAIL): 103 (96.3%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 34
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(low<high);aih_curated_blacklist: 2
  total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 1
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 1 fail (total: 5)
  low: 0 pass, 48 fail (total: 48)
  medium: 0 pass, 54 fail (total: 54)
Arriba filter: 107 rows -> 4 PASS; wrote tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00166_B23WHTKLT4_1.arriba.fusions.filter_summary.txt