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/de/631d213215caffdc849bd503d9c510/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/631d213215caffdc849bd503d9c510/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/2c84af6f25d71699c8c0e8ee2cf81d/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/a4e104adefad3ace452f4eeffb1179/aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2d4b78-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled