Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/4678714b8e162a7dbf4c6cced3c370/659_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/d65ed465f175f5538488cd32c35f64/659_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/b02a7396bf6caf366aae276126d7b9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/acaa52f0a1ee7e1ebbb59d6d1573d2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/acaa52f0a1ee7e1ebbb59d6d1573d2/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled