Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/9c5bdb7ad5baa0fee303a801c74c8f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/9c5bdb7ad5baa0fee303a801c74c8f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/fe7833070df3d0ba361381cf396a19/germline_control_2.haplotyper.split.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/d0857d433e70029d31731ae56e2eda/germline_control_2.mpileup.gz
==> STAGING COMPLETE (4 inputs)

Parsing mpileup: germline_control_2.mpileup.gz
Found 26 positions with indel observations
Annotating VCF: germline_control_2.haplotyper.split.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for 'germline_control_2.haplotyper.split.vcf.gz'
Output written to: germline_control_2.entropy.vcf