Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/0b22fe6c769c8c652d5c195a60bafb/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.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/bc/f2ffe15bfd712b2ebe23f121c987de/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/f2ffe15bfd712b2ebe23f121c987de/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/495df7c7d87251a4ec09c1d610db54/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000