Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/42e5f7fd394c48f1bd01d7b817d6ee/tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/bf28c36bc0d06b3ed4680b7330ce10/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/bf28c36bc0d06b3ed4680b7330ce10/.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 9 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 285
  Pass (FILTER=PASS): 28 (9.8%)
  Fail (FILTER=FAIL): 257 (90.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 54
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 38
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 22
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  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(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4

Breakdown by confidence:
  high: 28 pass, 6 fail (total: 34)
  low: 0 pass, 157 fail (total: 157)
  medium: 0 pass, 94 fail (total: 94)
Arriba filter: 285 rows -> 28 PASS; wrote tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00087_B23WHTKLT4_1.arriba.fusions.filter_summary.txt