Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/c30fee0f4d4d31e5fcd4101134c027/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/c30fee0f4d4d31e5fcd4101134c027/.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/7d/f6e5c17e00b45e5bb761583d06e39d/tih_rna_sample_00252_23H5VFLT4_s04.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: 314
  Pass (FILTER=PASS): 34 (10.8%)
  Fail (FILTER=FAIL): 280 (89.2%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 104
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 34
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 14
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 13
  confidence_below_min(low<high): 13
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 12
  confidence_below_min(low<high);total_reads_below_min(6.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(5.0<8.0): 10
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 8
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 7
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 3
  confidence_below_min(medium<high);aih_curated_blacklist: 3

Breakdown by confidence:
  high: 34 pass, 5 fail (total: 39)
  low: 0 pass, 111 fail (total: 111)
  medium: 0 pass, 164 fail (total: 164)
Arriba filter: 314 rows -> 34 PASS; wrote tih_rna_sample_00252_23H5VFLT4_s04.arriba.fusions.filtered.tsv and tih_rna_sample_00252_23H5VFLT4_s04.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00252_23H5VFLT4_s04.arriba.fusions.filter_summary.txt