Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/aec77973b89d81529313915b9c4e31/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/b9cfdcda882dd601b56358597c4c08/.command.sh
  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/1d/b9cfdcda882dd601b56358597c4c08/.command.run
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
processing BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam ... Finished