Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/004a12a7af3e1ecdb989b931a6b2a9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/e55c3b3c4fd0c449c87c4f1aa6f5ce/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/e55c3b3c4fd0c449c87c4f1aa6f5ce/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/d0a61d8e12285d291e64514b86f741/659_bqK_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/54710ccf84afb62882eaabb39a55a4/659_bqK_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bqK_T1_TRNA_1_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled