Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8b4cc11350ef208fe026d107d4bb47/tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/d02b934d1659c8abad5e8586d4c8d3/.command.sh
  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/e7/d02b934d1659c8abad5e8586d4c8d3/.command.run
  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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 220
  Pass (FILTER=PASS): 20 (9.1%)
  Fail (FILTER=FAIL): 200 (90.9%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 86
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 24
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 20
  confidence_below_min(low<high): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 5
  confidence_below_min(low<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(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  total_reads_below_min(7.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 20 pass, 1 fail (total: 21)
  low: 0 pass, 86 fail (total: 86)
  medium: 0 pass, 113 fail (total: 113)
Arriba filter: 220 rows -> 20 PASS; wrote tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.filtered.tsv and tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00121_23H5VFLT4_s41.arriba.fusions.filter_summary.txt