Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/a87d5950b2299f18ac9ac83abceffa/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/a87d5950b2299f18ac9ac83abceffa/.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/8a/ec324fec54e8183a8cadf847156cda/BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-13dfb8f7-c999-4ef0-9260-22ba79cf647d/75/c52a23060671398a8253a658f32ecc/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)
AIH curated blacklist: matched 3 fusion rows (breakpoint_ID in qualified set)
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ARRIBA FILTERING SUMMARY
================================================================================
Total fusions: 20
Pass (FILTER=PASS): 1 (5.0%)
Fail (FILTER=FAIL): 19 (95.0%)
AIH curated blacklist (blacklisted flag):
Total blacklisted: 3
All 3 blacklisted rows have FILTER=FAIL
Failure reasons (top 15):
confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 4
confidence_below_min(medium<high);aih_curated_blacklist: 2
confidence_below_min(medium<high): 2
confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 2
total_reads_below_min(7.0<8.0): 1
confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 1
Breakdown by confidence:
high: 1 pass, 1 fail (total: 2)
low: 0 pass, 13 fail (total: 13)
medium: 0 pass, 5 fail (total: 5)
Arriba filter: 20 rows -> 1 PASS; wrote BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.filtered.tsv and BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.filtered_pass_only.tsv
Summary written to: BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.filter_summary.txt