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/9c/e32bd963cba9c8db0b71b7c83867d1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/4384ffd54210c48ab7fc4bdeb3bb13/A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/e32bd963cba9c8db0b71b7c83867d1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/c9d08ed8bdfdb6136dc1aa50bd1fdb/A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
processing A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam ... Finished