Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/cc8c569db19f49dce85218b17e783c/tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/ed53cb18e9ed30a28da3c263ac6e6c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/ed53cb18e9ed30a28da3c263ac6e6c/.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: 181
  Pass (FILTER=PASS): 11 (6.1%)
  Fail (FILTER=FAIL): 170 (93.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 64
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 13
  confidence_below_min(low<high): 12
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(3.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 11 pass, 2 fail (total: 13)
  low: 0 pass, 62 fail (total: 62)
  medium: 0 pass, 106 fail (total: 106)
Arriba filter: 181 rows -> 11 PASS; wrote tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filtered.tsv and tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00467_B23WHTKLT4_2.arriba.fusions.filter_summary.txt