Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/5dcb3a60cc879aa3dfdadaf672eabb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/5dcb3a60cc879aa3dfdadaf672eabb/.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/b8/7fc4455d045f8e00c36492bf74dff4/tih_rna_sample_00414_23H5VFLT4_s40.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 226
  Pass (FILTER=PASS): 18 (8.0%)
  Fail (FILTER=FAIL): 208 (92.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 50
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 35
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 23
  confidence_below_min(low<high): 14
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<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): 4
  total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  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: 18 pass, 7 fail (total: 25)
  low: 0 pass, 104 fail (total: 104)
  medium: 0 pass, 97 fail (total: 97)
Arriba filter: 226 rows -> 18 PASS; wrote tih_rna_sample_00414_23H5VFLT4_s40.arriba.fusions.filtered.tsv and tih_rna_sample_00414_23H5VFLT4_s40.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00414_23H5VFLT4_s40.arriba.fusions.filter_summary.txt