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/16/42943cf820c3860bebdcaad7399d8c/1029_BH4B-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/58e53128791d384d3b7457e03ad5cd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/42943cf820c3860bebdcaad7399d8c/1029_BH4B-N1-BDNA-1_B23KGCJLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/58e53128791d384d3b7457e03ad5cd/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
==> STAGING COMPLETE (6 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1029_BH4B-N1-BDNA-1_B23KGCJLT4_1.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