Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/420c2a0cf5b37bcf5a661b99b51025/A673_FFPE_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/9f/b93ae192182f13a3655374d1671b38/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/b93ae192182f13a3655374d1671b38/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/993d7220d8446b61d7f0e428187633/A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000