Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/beeecd601555da06cc196226bc454c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/d41f8587033e95d5c234085ff7320a/tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/beeecd601555da06cc196226bc454c/.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 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 163
  Pass (FILTER=PASS): 23 (14.1%)
  Fail (FILTER=FAIL): 140 (85.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(medium<high): 8
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2
  total_reads_below_min(7.0<8.0): 2
  total_reads_below_min(5.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 23 pass, 6 fail (total: 29)
  low: 0 pass, 57 fail (total: 57)
  medium: 0 pass, 77 fail (total: 77)
Arriba filter: 163 rows -> 23 PASS; wrote tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00149_B23WHTKLT4_1.arriba.fusions.filter_summary.txt