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/fc/6be17f010975f650e581beee2cff8f/.command.sh
  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_annot.gtf
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/6be17f010975f650e581beee2cff8f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/3b7f45ba2b342f7f7d5c8d323cd4ed/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

[2026-06-08T08:58:46] Launching Arriba 2.4.0
[2026-06-08T08:58:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:55] Reading chimeric alignments from 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=WARNING: 92580598)
2893601 SAM records were malformed and ignored
[2026-06-08T09:09:39] Marking multi-mapping alignments (marked=86112847)
[2026-06-08T09:10:04] Detecting strandedness (no)
[2026-06-08T09:10:04] Annotating alignments