Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/344a766123d491680ca1f256f493ce/659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/f95daf23d5998a64667aa4ddf37cb4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/f95daf23d5998a64667aa4ddf37cb4/.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-0c31b8cc-cacb-407a-8f2b-eb2d8317e249/e8/83b3d86dc9f1df6763490ba67ef20d/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 5 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 263
  Pass (FILTER=PASS): 5 (1.9%)
  Fail (FILTER=FAIL): 258 (98.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 5
  All 5 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 63
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 44
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 15
  confidence_below_min(low<high): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 4

Breakdown by confidence:
  high: 5 pass, 1 fail (total: 6)
  low: 0 pass, 118 fail (total: 118)
  medium: 0 pass, 139 fail (total: 139)
Arriba filter: 263 rows -> 5 PASS; wrote 659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv and 659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_1q-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt