Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/000e73180f411295ee953841de045c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/000e73180f411295ee953841de045c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/e4214c44367f5a722b96617268e124/tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.tsv
  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-7324c8a8-f474-426a-a5c9-715912777f94/d8/92d6652b0b8fcc763d0f3fff270437/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 315
  Pass (FILTER=PASS): 40 (12.7%)
  Fail (FILTER=FAIL): 275 (87.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 58
  confidence_below_min(medium<high): 57
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high): 20
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 40 pass, 4 fail (total: 44)
  low: 0 pass, 138 fail (total: 138)
  medium: 0 pass, 133 fail (total: 133)
Arriba filter: 315 rows -> 40 PASS; wrote tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.filtered.tsv and tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00693_B23MVV7LT4_1.arriba.fusions.filter_summary.txt