Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/b32f1613cc5cc643875b9ddf6bf94e/659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/03cafb423c59e14fcbd4a149a5cb07/659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  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/87/1317de6ba46546700c3271d81ba7e5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/1317de6ba46546700c3271d81ba7e5/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_1q-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