Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/8aae36ea89e1e915bfd3f78e9a7d69/tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/6bc91b3ae3b591d9bc7c76b613d866/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/6bc91b3ae3b591d9bc7c76b613d866/.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 195
  Pass (FILTER=PASS): 29 (14.9%)
  Fail (FILTER=FAIL): 166 (85.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 49
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 18
  confidence_below_min(low<high): 10
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(6.0<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(7.0<8.0): 2

Breakdown by confidence:
  high: 29 pass, 2 fail (total: 31)
  low: 0 pass, 74 fail (total: 74)
  medium: 0 pass, 90 fail (total: 90)
Arriba filter: 195 rows -> 29 PASS; wrote tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.filtered.tsv and tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00377_23H5VFLT4_s23.arriba.fusions.filter_summary.txt