Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/771e973e5ee9d15f368533938fbcb5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/771e973e5ee9d15f368533938fbcb5/.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/06/45874b5df6136ccadec43c19279b54/tih_rna_sample_00394_23H5VFLT4_s25.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 6 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 149
  Pass (FILTER=PASS): 9 (6.0%)
  Fail (FILTER=FAIL): 140 (94.0%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 27
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 10
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  total_reads_below_min(5.0<8.0): 4
  confidence_below_min(medium<high);aih_curated_blacklist: 4
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 4
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 4
  total_reads_below_min(6.0<8.0): 3
  total_reads_below_min(4.0<8.0): 3

Breakdown by confidence:
  high: 9 pass, 15 fail (total: 24)
  low: 0 pass, 64 fail (total: 64)
  medium: 0 pass, 61 fail (total: 61)
Arriba filter: 149 rows -> 9 PASS; wrote tih_rna_sample_00394_23H5VFLT4_s25.arriba.fusions.filtered.tsv and tih_rna_sample_00394_23H5VFLT4_s25.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00394_23H5VFLT4_s25.arriba.fusions.filter_summary.txt