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/f9/9b7e7b2ef1237e3e9faba4ba632e7a/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/53e97f96f363bd4dcfba9a17ce7e41/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/53e97f96f363bd4dcfba9a17ce7e41/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/1b6839c2f11fb05d655d02c6eec5b1/A549_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Finished
Total 58841 usable reads were sampled