Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5fdcfd213e70a9a0fe664de13f2dc6/tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/9a7e22f7fcac37297b0fcdf4e8b64d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/9a7e22f7fcac37297b0fcdf4e8b64d/.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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 248
  Pass (FILTER=PASS): 11 (4.4%)
  Fail (FILTER=FAIL): 237 (95.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 60
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 46
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 25
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(low<high): 12
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  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): 4
  aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 2

Breakdown by confidence:
  high: 11 pass, 4 fail (total: 15)
  low: 0 pass, 119 fail (total: 119)
  medium: 0 pass, 114 fail (total: 114)
Arriba filter: 248 rows -> 11 PASS; wrote tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.filtered.tsv and tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00280_23H5VFLT4_s18.arriba.fusions.filter_summary.txt