Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/3171500a50c9bd5080263632153746/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/3171500a50c9bd5080263632153746/.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/27/c694df4fd01b39464076bab22721ea/tih_rna_sample_00111_23H5VFLT4_s30.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 3 fusion rows (breakpoint_ID in qualified set)
================================================================================
ARRIBA FILTERING SUMMARY
================================================================================
Total fusions: 46
Pass (FILTER=PASS): 2 (4.3%)
Fail (FILTER=FAIL): 44 (95.7%)
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(5.0<8.0): 10
confidence_below_min(medium<high): 7
confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 6
confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 6
confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 3
confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 3
confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 2
total_reads_below_min(3.0<8.0): 2
confidence_below_min(medium<high);aih_curated_blacklist: 2
confidence_below_min(low<high);total_reads_below_min(4.0<8.0): 2
confidence_below_min(medium<high);total_reads_below_min(3.0<8.0);aih_curated_blacklist: 1
Breakdown by confidence:
high: 2 pass, 2 fail (total: 4)
low: 0 pass, 26 fail (total: 26)
medium: 0 pass, 16 fail (total: 16)
Arriba filter: 46 rows -> 2 PASS; wrote tih_rna_sample_00111_23H5VFLT4_s30.arriba.fusions.filtered.tsv and tih_rna_sample_00111_23H5VFLT4_s30.arriba.fusions.filtered_pass_only.tsv
Summary written to: tih_rna_sample_00111_23H5VFLT4_s30.arriba.fusions.filter_summary.txt