Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/abb7c846b0f04c0a1d773f1ba4ef9a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/abb7c846b0f04c0a1d773f1ba4ef9a/.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/d3/fc8417d3a40f787e476ddfb0ceba32/659_cRa-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-bba2394f-ea06-4038-829e-f0bb41c45b0f/84/e510984b93930338ae941c5c84bcbe/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 256
  Pass (FILTER=PASS): 25 (9.8%)
  Fail (FILTER=FAIL): 231 (90.2%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 6
  All 6 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 78
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 23
  confidence_below_min(low<high);total_reads_below_min(3.0<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(2.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  confidence_below_min(low<high): 7
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 6
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  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(low<high);total_reads_below_min(7.0<8.0): 3

Breakdown by confidence:
  high: 25 pass, 6 fail (total: 31)
  low: 0 pass, 88 fail (total: 88)
  medium: 0 pass, 137 fail (total: 137)
Arriba filter: 256 rows -> 25 PASS; wrote 659_cRa-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered.tsv and 659_cRa-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cRa-T1-TRNA-1_A23MVY2LT4_1.arriba.fusions.filter_summary.txt