Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/75eea3aa40c94795d764a1fed37435/Filler-D0002999.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/75eea3aa40c94795d764a1fed37435/Filler-D0002999.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/6fe3daac1e2c56cf179c2c1ad7dc42/.command.sh
  Downloading: s3://natera-platform-sandbox/projects/lcvs/bed-files/prenatal-exome-v1-targets-hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/6fe3daac1e2c56cf179c2c1ad7dc42/.command.run
==> STAGING COMPLETE (6 inputs)

[W::hts_idx_load3] The index file is older than the data file: Filler-D0002999.md.bam.bai
ls: cannot access '*.per-base.d4': No such file or directory
ls: cannot access '*.quantized.bed.gz': No such file or directory
ls: cannot access '*.quantized.bed.gz.csi': No such file or directory
ls: cannot access '*.thresholds.bed.gz': No such file or directory
ls: cannot access '*.thresholds.bed.gz.csi': No such file or directory