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/88/0323c5453cb062488ff161a507e69e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/6a6841fce8fea2344ff1577a07a0ad/SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  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/88/0323c5453cb062488ff161a507e69e/.command.run
==> STAGING COMPLETE (8 inputs)

[2026-05-28T23:29:57] Launching Arriba 2.4.0
[2026-05-28T23:29:57] Loading assembly from 'ref_genome.fa' 
[2026-05-28T23:30:11] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T23:30:14] Reading chimeric alignments from 'SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam'