Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/9432b492030b76af3248c3b7e8a412/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/a468fe33321ec2f592004e83ccc3bc/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/ca4d20e41802bc8c33ea65523f74cb/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/cb2b4288c80cd1e810575cad11dbd3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/cb2b4288c80cd1e810575cad11dbd3/.command.run
==> STAGING COMPLETE (5 inputs)

processing ref_annot.bed ... Done
[W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
processing 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam ... Finished