Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/45b4611e0e84f1398fa97b4879d974/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/ffcae09cb11657715a509b26115a7f/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/09db4e1c8d428de128611f58d8585c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/09db4e1c8d428de128611f58d8585c/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Done
Total read pairs  used 49482