Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/38d5ed4138585a1be7d08a077f1302/SW780_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  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/d8/2fa1541d6f6632c886a1dfeb279507/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/2fa1541d6f6632c886a1dfeb279507/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/29edf251c411380fa1ce53fa166ed7/SW780_FFPE_RNA_0001_B23LG7FLT4_1.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