Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/0243baf59143a09530ee8911e13e43/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/689bd213f9a1ac87c0897aeb988277/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/689bd213f9a1ac87c0897aeb988277/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/dde4de080fccda79d1586d5ef24e0f/659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/ecd326546f2f66e7990b3d1c9b38e3/659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bKP-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