Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/3294f66d1a7091efa35305a2c6f248/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/3294f66d1a7091efa35305a2c6f248/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/8f087cbb5133786b1e7a44c3e22ff2/tih_rna_sample_00097_23H5VFLT4_s12.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-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 7 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 330
  Pass (FILTER=PASS): 44 (13.3%)
  Fail (FILTER=FAIL): 286 (86.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 7
  All 7 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 70
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 42
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high): 11
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<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(6.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 3

Breakdown by confidence:
  high: 44 pass, 6 fail (total: 50)
  low: 0 pass, 115 fail (total: 115)
  medium: 0 pass, 165 fail (total: 165)
Arriba filter: 330 rows -> 44 PASS; wrote tih_rna_sample_00097_23H5VFLT4_s12.arriba.fusions.filtered.tsv and tih_rna_sample_00097_23H5VFLT4_s12.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00097_23H5VFLT4_s12.arriba.fusions.filter_summary.txt