Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/34e899494ccdd52e2cf87145d46cfa/dna_s755.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/004a12a7af3e1ecdb989b931a6b2a9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/e2f626e7ed769a8ec599b0149d8787/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/e2f626e7ed769a8ec599b0149d8787/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/b8016cdae8287ee69f0d17c27f35bb/dna_s755.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: dna_s755.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000