Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/9e0fc25353582bd7fba9463241580b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/15/9e0fc25353582bd7fba9463241580b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/65f06cd3e9e66d1e34a7491dc5105b/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e106d13faaf71d982b3721a6e6dcf1/BreastNB_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: BreastNB_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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