Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/23677ccc4d2b40c8b99bdeb5215367/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/cac338698952731907b7584bf502c1/A549_FFPE_01_RNA_0001_B23LG7FLT4_2.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/a2/05ff64539df568d03458231e9a50cf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/05ff64539df568d03458231e9a50cf/.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_2.Aligned.sortedByCoord.out.bam.bai
Reading reference gene model ref_annot.bed ... Done
Loading SAM/BAM file ...  Finished
Total 25453 usable reads were sampled