Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/6473f93792e6b59771d5b56f358827/positive_somatic_control_2.snv_indel.strelka.indel.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/6473f93792e6b59771d5b56f358827/positive_somatic_control_2.snv_indel.strelka.indel.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/e7d25a68c893bcd1b666dfeb7b233e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/1a71006382d0056b426775f6041d6a/positive_somatic_control_2.snv_indel.tnseq.snv.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/e7d25a68c893bcd1b666dfeb7b233e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/1a71006382d0056b426775f6041d6a/positive_somatic_control_2.snv_indel.tnseq.snv.vcf.gz
==> STAGING COMPLETE (6 inputs)

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