Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/aac47622e0b29a175beeedd6e62a80/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/e37536ddd98d1b370c1b7c49140f48/positive_somatic_control_2.snv_indel.whatshap.chr5.phased.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/aac47622e0b29a175beeedd6e62a80/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/7c2e3351618d2405cd738ec10c608a/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