Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/bc3511b1058923acd74df9095d98ed/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/bc3511b1058923acd74df9095d98ed/.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/d4/7445855e676d390b9684a0a72ed4c1/tih_rna_sample_00736_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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 203
  Pass (FILTER=PASS): 22 (10.8%)
  Fail (FILTER=FAIL): 181 (89.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 28
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 18
  confidence_below_min(medium<high): 15
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 22 pass, 2 fail (total: 24)
  low: 0 pass, 97 fail (total: 97)
  medium: 0 pass, 82 fail (total: 82)
Arriba filter: 203 rows -> 22 PASS; wrote tih_rna_sample_00736_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00736_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00736_B23MVV7LT4_1.arriba.fusions.filter_summary.txt