Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/f449d8b120a24e15822fc7eb25ef75/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f789d11d3dfd58975ba1c1dd754edc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/12eea7b6850336648970fd25510451/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/4179bca64d0780950358b97c82e8f0/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/12eea7b6850336648970fd25510451/.command.run
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
processing 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam ... Finished