Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/460466ccbd3517ac60b630c99be2b0/tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/e0193245d791c3b0cd76250f4a2bd7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/e0193245d791c3b0cd76250f4a2bd7/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 185
  Pass (FILTER=PASS): 8 (4.3%)
  Fail (FILTER=FAIL): 177 (95.7%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 79
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2
  aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2

Breakdown by confidence:
  high: 8 pass, 2 fail (total: 10)
  low: 0 pass, 65 fail (total: 65)
  medium: 0 pass, 110 fail (total: 110)
Arriba filter: 185 rows -> 8 PASS; wrote tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.filtered.tsv and tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00403_23H5VFLT4_s29.arriba.fusions.filter_summary.txt