Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/7d689d02309ab4996dad6f89d912a0/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/e88fd7fc7045f143707b3a331bf8bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/77fbea2a8a614d71322af94d628d60/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/77fbea2a8a614d71322af94d628d60/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/14a19fb5f4ba677d8c6d6065a18b8f/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled