Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f789d11d3dfd58975ba1c1dd754edc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/49c175607bf010cbf80ea54553d318/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/369a4c1784fa5c8c1eb6124589dba9/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/49c175607bf010cbf80ea54553d318/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/e750b7e0760a212602dfae8d940a92/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 17152373
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	17152373
Known Splicing Events:	16784245
Partial Novel Splicing Events:	75308
Novel Splicing Events:	275803
Filtered Splicing Events:	17017

Total splicing  Junctions:	100995
Known Splicing Junctions:	95240
Partial Novel Splicing Junctions:	2123
Novel Splicing Junctions:	3632

===================================================================
Create BED file ...
Create Interact file ...