Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/e88fd7fc7045f143707b3a331bf8bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/15ed5a12593db27008c3c6f4c535de/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/15ed5a12593db27008c3c6f4c535de/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/1d979abaed073c06b5748fbff6148d/tih_rna_sample_00570_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/55c6f603edda9326c80d16dcf29b08/tih_rna_sample_00570_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00570_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000