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/2b/c5cad9304aa11abc222dd767ae020e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/c5cad9304aa11abc222dd767ae020e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/277f3765410927d3d2b7f9179bf5ef/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/9967085c1a3af0ed4453d838ec66b2/1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
==> 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