Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/99c40323c241ef8c796831fa72cffc/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/7f6cf51997f4908dd901e6cb280773/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  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/71/a811bab92014e41327047e94c49540/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/a811bab92014e41327047e94c49540/.command.run
==> STAGING COMPLETE (5 inputs)

ls: *.sam: No such file or directory
ls: *.csi: No such file or directory
ls: *.crai: No such file or directory