Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/2dad3b3322577612401e31c91889d7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/2dad3b3322577612401e31c91889d7/.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/3a/05da3385264a29e4ac6dd578ad9318/tih_rna_sample_00088_23H5VFLT4_s02.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 10 fusion rows (breakpoint_ID in qualified set)

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

Total fusions: 183
  Pass (FILTER=PASS): 10 (5.5%)
  Fail (FILTER=FAIL): 173 (94.5%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 10
  All 10 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 66
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 18
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high): 8
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 7
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
  total_reads_below_min(3.0<8.0): 2
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 2
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 2

Breakdown by confidence:
  high: 10 pass, 5 fail (total: 15)
  low: 0 pass, 73 fail (total: 73)
  medium: 0 pass, 95 fail (total: 95)
Arriba filter: 183 rows -> 10 PASS; wrote tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.filtered.tsv and tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00088_23H5VFLT4_s02.arriba.fusions.filter_summary.txt