Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/b4b9675ee8a50d7c8edf4442ee8d79/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/b4b9675ee8a50d7c8edf4442ee8d79/.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/2b/1bc3de212560edc0faddaf7dc391a2/tih_rna_sample_00096_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 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 206
  Pass (FILTER=PASS): 26 (12.6%)
  Fail (FILTER=FAIL): 180 (87.4%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 26
  confidence_below_min(medium<high): 25
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  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(6.0<8.0): 3

Breakdown by confidence:
  high: 26 pass, 2 fail (total: 28)
  low: 0 pass, 81 fail (total: 81)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 206 rows -> 26 PASS; wrote tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00096_B23WHTKLT4_1.arriba.fusions.filter_summary.txt