Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/749a29b28bfe5eedcab41e00e9e114/tih_rna_sample_00274_23H5VFLT4_s14.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/cefd1198fb4904b940359099ca000b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/cefd1198fb4904b940359099ca000b/.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/stage-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 80
  Pass (FILTER=PASS): 6 (7.5%)
  Fail (FILTER=FAIL): 74 (92.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(medium<high): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0);aih_curated_blacklist: 1

Breakdown by confidence:
  high: 6 pass, 2 fail (total: 8)
  low: 0 pass, 55 fail (total: 55)
  medium: 0 pass, 17 fail (total: 17)
Arriba filter: 80 rows -> 6 PASS; wrote tih_rna_sample_00274_23H5VFLT4_s14.arriba.fusions.filtered.tsv and tih_rna_sample_00274_23H5VFLT4_s14.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00274_23H5VFLT4_s14.arriba.fusions.filter_summary.txt