Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/794c2d8f7534502d93801659950f5d/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/74fac6d403e2bdcff34a202ecfd354/1173_BEE_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/3e/2927503cb47c29475c5567e35c96c8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/2927503cb47c29475c5567e35c96c8/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_BEE_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