Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/ddf4c98689a53bf8fc8638d176b5de/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/cac295b3aed90f27044a3fe37de8dc/positive_somatic_control_2.snv_indel.whatshap.chr5.phased.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/ddf4c98689a53bf8fc8638d176b5de/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/dc6639c9053885b3dc33ec5ec15804/positive_somatic_control_2.snv_indel.whatshap.chr21.phased.vcf.gz
==> STAGING COMPLETE (4 inputs)

Checking the headers and starting positions of 2 files
ls: positive_somatic_control_2.snv_indel.phased.vcf.gz.csi: No such file or directory