Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/projects/lcvs/bed-files/xgen-exome-research-panel-v2-targets-hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/23bedc9b57434a729fdf0b5fd0cef1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/23bedc9b57434a729fdf0b5fd0cef1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/479d3d9b7683c8a039a55de9bc9438/D0001109_22q.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/479d3d9b7683c8a039a55de9bc9438/D0001109_22q.md.bam
==> STAGING COMPLETE (6 inputs)

[W::hts_idx_load3] The index file is older than the data file: D0001109_22q.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