Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/32db3ef66d5686d240f32e97fa96c8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/32db3ef66d5686d240f32e97fa96c8/.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/42/4334783557d10c37b44a396f33b7f1/tih_rna_sample_00087_23H5VFLT4_s17.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 14 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 309
  Pass (FILTER=PASS): 33 (10.7%)
  Fail (FILTER=FAIL): 276 (89.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 14
  All 14 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 68
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 35
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 27
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 21
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 20
  confidence_below_min(low<high): 18
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 15
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(medium<high);aih_curated_blacklist: 7
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(low<high);total_reads_below_min(7.0<8.0): 5
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 4

Breakdown by confidence:
  high: 33 pass, 2 fail (total: 35)
  low: 0 pass, 157 fail (total: 157)
  medium: 0 pass, 117 fail (total: 117)
Arriba filter: 309 rows -> 33 PASS; wrote tih_rna_sample_00087_23H5VFLT4_s17.arriba.fusions.filtered.tsv and tih_rna_sample_00087_23H5VFLT4_s17.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00087_23H5VFLT4_s17.arriba.fusions.filter_summary.txt