Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/8f5870620f44ddfce17543a11aa0b0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/d52a64f91e5d1c3aec81f40ecb81be/tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/8f5870620f44ddfce17543a11aa0b0/.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 280
  Pass (FILTER=PASS): 19 (6.8%)
  Fail (FILTER=FAIL): 261 (93.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 89
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 43
  confidence_below_min(low<high): 24
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 16
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  total_reads_below_min(3.0<8.0): 4

Breakdown by confidence:
  high: 19 pass, 7 fail (total: 26)
  low: 0 pass, 128 fail (total: 128)
  medium: 0 pass, 126 fail (total: 126)
Arriba filter: 280 rows -> 19 PASS; wrote tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.filtered.tsv and tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00248_23H5VFLT4_s01.arriba.fusions.filter_summary.txt