Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/1ec2ee5aefa5681d6be712733c08c1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/1ec2ee5aefa5681d6be712733c08c1/.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/83/633ec2d2f556ae8ef827c00d46368f/tih_rna_sample_00090_23H5VFLT4_s32.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 8 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 187
  Pass (FILTER=PASS): 11 (5.9%)
  Fail (FILTER=FAIL): 176 (94.1%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 8
  All 8 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 26
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 22
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 16
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 3
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 11 pass, 0 fail (total: 11)
  low: 0 pass, 81 fail (total: 81)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 187 rows -> 11 PASS; wrote tih_rna_sample_00090_23H5VFLT4_s32.arriba.fusions.filtered.tsv and tih_rna_sample_00090_23H5VFLT4_s32.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00090_23H5VFLT4_s32.arriba.fusions.filter_summary.txt