Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/8f45fd2eb51d82dd397ffdc1de7cdc/659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/e640dac831905516eb931426ebee99/659_bGc-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/9b/8aacd110f671b20afbb0c40629a08c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/8aacd110f671b20afbb0c40629a08c/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled