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/fa/43c3581820b75fcc5a5e6b625d60d9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/43c3581820b75fcc5a5e6b625d60d9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/6e0d341d42a94f49161252cef23de5/659_6i-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/d7dc18735f2e3f21179ef8f3c52ccd/659_6i-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_6i-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