Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/0c95ee27a3afbad9e361a65c31958d/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/10bb890d2eee930d920cb0d625bfbd/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/4a82c3761ae9a77f263f0d33106444/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/4a82c3761ae9a77f263f0d33106444/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled