Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/a928b0104ce2a0c5aab1aa187fc2fb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/a928b0104ce2a0c5aab1aa187fc2fb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/efa3b73c092271724cd40f2f167eac/659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv
  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-99ebc9bd-f9f1-4b2c-b9a0-02ddaf99f257/ee/adda01b2d23fdd27de06edfd21ea26/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 1 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 60
  Pass (FILTER=PASS): 4 (6.7%)
  Fail (FILTER=FAIL): 56 (93.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 1
  All 1 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 7
  total_reads_below_min(4.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 5
  total_reads_below_min(3.0<8.0): 4
  confidence_below_min(medium<high): 4
  total_reads_below_min(7.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 1
  total_reads_below_min(6.0<8.0): 1
  total_reads_below_min(5.0<8.0): 1
  total_reads_below_min(4.0<8.0);aih_curated_blacklist: 1
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 1
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 1

Breakdown by confidence:
  high: 4 pass, 14 fail (total: 18)
  low: 0 pass, 24 fail (total: 24)
  medium: 0 pass, 18 fail (total: 18)
Arriba filter: 60 rows -> 4 PASS; wrote 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered.tsv and 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_Dl-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.filter_summary.txt