Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/4a48430ada3cad8104f36bc69957cf/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/4a48430ada3cad8104f36bc69957cf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/fb89939eba61d5b706cbb1ad481589/aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

[2026-06-08T09:35:05] Launching Arriba 2.4.0
[2026-06-08T09:35:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:35:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:35:18] Reading chimeric alignments from 'aih-tih-sc-2a5468-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam'