Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ebb8d66d0e4680eaed709c7ce41c82/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/67bbc846f38bc21da9b9f0f12484bc/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/67bbc846f38bc21da9b9f0f12484bc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d20a971c93be1dc46f16704254326/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (4 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Load BAM file ...  Done
report duplicte rate based on sequence ...
report duplicte rate based on mapping  ...
generate R script ...
null device 
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