Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/ac8b1eaf7821ffd60f3b23b69cdca6/A673_FFPE_RNA_0001_B23LG7FLT4_3.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/5c/ae0ffb9c4ee3ff6c2c6d0b94100d54/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/ae0ffb9c4ee3ff6c2c6d0b94100d54/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2019f56f93e4025d3ff4dd0e34946d/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled