Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/9e6476ff3693cb39680fd279d1ebb8/tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/210338cca569dca6ffa6f4712ad528/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/210338cca569dca6ffa6f4712ad528/.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-5b456d70-fab3-4fcc-916c-bc437f411fba/48/d36e0303d259ad82d7d96e756f6134/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 11 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 270
  Pass (FILTER=PASS): 39 (14.4%)
  Fail (FILTER=FAIL): 231 (85.6%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 11
  All 11 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 74
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 16
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 3
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 2

Breakdown by confidence:
  high: 39 pass, 3 fail (total: 42)
  low: 0 pass, 100 fail (total: 100)
  medium: 0 pass, 128 fail (total: 128)
Arriba filter: 270 rows -> 39 PASS; wrote tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.filtered.tsv and tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00124_23H5VFLT4_s31.arriba.fusions.filter_summary.txt