Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/86b7b3c47be941bd270e159a744665/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/86b7b3c47be941bd270e159a744665/.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/d6/f905c43bd7f721963947e6dd1ec0c1/tih_rna_sample_00599_B23MVV7LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/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: 279
  Pass (FILTER=PASS): 33 (11.8%)
  Fail (FILTER=FAIL): 246 (88.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 80
  confidence_below_min(low<high): 27
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 17
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 33 pass, 12 fail (total: 45)
  low: 0 pass, 113 fail (total: 113)
  medium: 0 pass, 121 fail (total: 121)
Arriba filter: 279 rows -> 33 PASS; wrote tih_rna_sample_00599_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00599_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00599_B23MVV7LT4_1.arriba.fusions.filter_summary.txt