Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/d205c7252293e9bff5dcdf245b803d/.command.sh
  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/9b/bee10aa702195de1e8c3898ba03a5a/tih_rna_sample_00581_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/08bf324c3cf25aebafe8407e410b94/tih_rna_sample_00581_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/d205c7252293e9bff5dcdf245b803d/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00581_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Total 200000 usable reads were sampled