Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/ade8fd0ae6f3c91e6aa59626dad0ef/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/ade8fd0ae6f3c91e6aa59626dad0ef/.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/f6/40afff90874ef849b8d7657e8f8113/tih_rna_sample_00254_23H5VFLT4_s05.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 12 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 181
  Pass (FILTER=PASS): 5 (2.8%)
  Fail (FILTER=FAIL): 176 (97.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 12
  All 12 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 27
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 20
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5

Breakdown by confidence:
  high: 5 pass, 4 fail (total: 9)
  low: 0 pass, 76 fail (total: 76)
  medium: 0 pass, 96 fail (total: 96)
Arriba filter: 181 rows -> 5 PASS; wrote tih_rna_sample_00254_23H5VFLT4_s05.arriba.fusions.filtered.tsv and tih_rna_sample_00254_23H5VFLT4_s05.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00254_23H5VFLT4_s05.arriba.fusions.filter_summary.txt