Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ead7548c923424c68495c616845975/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/cef30cafe86caa5c61b8efcb1ffce8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/5e6db1165b7fd12c35ab76c4569de3/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/cef30cafe86caa5c61b8efcb1ffce8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/69/282e3130ec2b5936f2c532e47d0011/659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bTo-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled