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/f7/c23bef1c8563ff049bab845cd5cd0a/.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/f7/c23bef1c8563ff049bab845cd5cd0a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/abf35c9b8a6909eca5c16eef2c6d8c/FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

[2026-05-28T21:25:48] Launching Arriba 2.4.0
[2026-05-28T21:25:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:26:04] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:26:10] Reading chimeric alignments from 'FFPE_HD789_01_RNA_0002_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=WARNING: 91201 SAM records were malformed and ignored
12178660)
[2026-05-28T21:38:42] Marking multi-mapping alignments (marked=8315155)
[2026-05-28T21:38:49] Detecting strandedness (reverse)
[2026-05-28T21:38:49] Assigning strands to alignments 
[2026-05-28T21:38:53] Annotating alignments