Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/04c4c44ea17fe7421b72d5f28c777c/659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/b02a7396bf6caf366aae276126d7b9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/920831ba1447e7513ba90b63e9e842/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/920831ba1447e7513ba90b63e9e842/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/596dc83cd135ae3e53e2e69434618e/659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000