Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ebb454649b9ac609ab407d41fec8e2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  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/32/b0ec13f780e0b7021bcd5f9bbad0e4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/31c39c8f066eda72f7e73d301df784/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/b0ec13f780e0b7021bcd5f9bbad0e4/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Get exon regions from ref_annot.bed ...
Load BAM file ...  Total read pairs  used 1000000