Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/363eba166e988cf76c8e6b793254d1/1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/29ca77f36ab860afe08eb798428957/1173_FM_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/32/992f15828e51e443ee82c01f15d0c9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/992f15828e51e443ee82c01f15d0c9/.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_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
processing 1173_FM_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam ... Finished