Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/c6b914776742968a7a6f9a3a481803/aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a4/0352010e5727c976f7d16ce88a08da/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/d8491fd805df882db6602bbbb54296/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/d8491fd805df882db6602bbbb54296/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/634be424d910e31b5cd0f516a38eb6/aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000