Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/a7b5f35cd2b17e0607b464fdb21009/tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/a636e9ac17dcae954d8d08ecbcc868/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/53/a636e9ac17dcae954d8d08ecbcc868/.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 4 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 183
  Pass (FILTER=PASS): 7 (3.8%)
  Fail (FILTER=FAIL): 176 (96.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 4
  All 4 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 88
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 2

Breakdown by confidence:
  high: 7 pass, 0 fail (total: 7)
  low: 0 pass, 69 fail (total: 69)
  medium: 0 pass, 107 fail (total: 107)
Arriba filter: 183 rows -> 7 PASS; wrote tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.filtered.tsv and tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00116_23H5VFLT4_s36.arriba.fusions.filter_summary.txt