Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/5d6fc876c16ba284d60eee2cd75675/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
  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/70/0efb75e967625d3ec44c4a38c9c8ef/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/2f8b76f8eef9c6ab2c47588011c787/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/0efb75e967625d3ec44c4a38c9c8ef/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled