Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8d79467cc774a2b6e2d8871f53b880/.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/c4/8d79467cc774a2b6e2d8871f53b880/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/c66181a1a3c62cfa01b9a28fb4f82e/tih_rna_sample_00388_23H5VFLT4_s22.arriba.fusions.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 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 290
  Pass (FILTER=PASS): 54 (18.6%)
  Fail (FILTER=FAIL): 236 (81.4%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 67
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 25
  confidence_below_min(low<high): 18
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 9
  confidence_below_min(medium<high);aih_curated_blacklist: 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3

Breakdown by confidence:
  high: 54 pass, 7 fail (total: 61)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 118 fail (total: 118)
Arriba filter: 290 rows -> 54 PASS; wrote tih_rna_sample_00388_23H5VFLT4_s22.arriba.fusions.filtered.tsv and tih_rna_sample_00388_23H5VFLT4_s22.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00388_23H5VFLT4_s22.arriba.fusions.filter_summary.txt