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/5b/c426f07dda69f4c7f53d61904cddda/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/78b9b7248ed477c45cdc4cbb1b53b1/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/c426f07dda69f4c7f53d61904cddda/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5d298b7528f78dc4019c240b840ae9/1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_CH0_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled