Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/a77cadb4c7a2bcefd36a56e7e499ec/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/cd86966b934f371f3d4ca5156ceec4/tih_rna_sample_00118_23H5VFLT4_s38.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/a77cadb4c7a2bcefd36a56e7e499ec/.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 255
  Pass (FILTER=PASS): 34 (13.3%)
  Fail (FILTER=FAIL): 221 (86.7%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 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): 29
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 7
  confidence_below_min(low<high): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 34 pass, 6 fail (total: 40)
  low: 0 pass, 115 fail (total: 115)
  medium: 0 pass, 100 fail (total: 100)
Arriba filter: 255 rows -> 34 PASS; wrote tih_rna_sample_00118_23H5VFLT4_s38.arriba.fusions.filtered.tsv and tih_rna_sample_00118_23H5VFLT4_s38.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00118_23H5VFLT4_s38.arriba.fusions.filter_summary.txt