Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/794c2d8f7534502d93801659950f5d/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/74fac6d403e2bdcff34a202ecfd354/1173_BEE_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/8253cd84841d9f809bc9ae8deaa3ca/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/8253cd84841d9f809bc9ae8deaa3ca/.command.run
==> STAGING COMPLETE (4 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_BEE_T1_RNA_SLD_01_A23T55JLT4_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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