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/c2/6031e5e71766dfe9888f85d1c3a9e4/.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/c2/6031e5e71766dfe9888f85d1c3a9e4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/fa2ecb20fa04e52f80fe0567c49508/OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

[2026-05-28T21:56:32] Launching Arriba 2.4.0
[2026-05-28T21:56:32] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:56:44] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:56:48] Reading chimeric alignments from 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' WARNING: 2893601 SAM records were malformed and ignored
(total=92580598)
[2026-05-28T22:13:18] Marking multi-mapping alignments (marked=86112847)
[2026-05-28T22:13:47] Detecting strandedness (no)
[2026-05-28T22:13:47] Annotating alignments