Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/aa215f1081d2b9f50e219de6d56656/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/aa215f1081d2b9f50e219de6d56656/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/c098772ea9972bff425fa388858d0c/tih_rna_sample_00261_23H5VFLT4_s06.arriba.fusions.tsv
  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: 249
  Pass (FILTER=PASS): 35 (14.1%)
  Fail (FILTER=FAIL): 214 (85.9%)

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

Failure reasons (top 15):
  confidence_below_min(medium<high): 53
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 22
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 21
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 19
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 19
  confidence_below_min(low<high): 11
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 11
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 11
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 8
  confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 6
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 5
  confidence_below_min(medium<high);aih_curated_blacklist: 5
  total_reads_below_min(3.0<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(6.0<8.0): 2

Breakdown by confidence:
  high: 35 pass, 9 fail (total: 44)
  low: 0 pass, 99 fail (total: 99)
  medium: 0 pass, 106 fail (total: 106)
Arriba filter: 249 rows -> 35 PASS; wrote tih_rna_sample_00261_23H5VFLT4_s06.arriba.fusions.filtered.tsv and tih_rna_sample_00261_23H5VFLT4_s06.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00261_23H5VFLT4_s06.arriba.fusions.filter_summary.txt