Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/3f5ec9f0a169d4d484b81b4e99fa4e/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/bc/8b8cd2c5093b77443c3c29f93530b7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/8b8cd2c5093b77443c3c29f93530b7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/71117a58f0b32aa82ed8ea882f6136/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 16738167
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	16738167
Known Splicing Events:	16559710
Partial Novel Splicing Events:	80571
Novel Splicing Events:	84182
Filtered Splicing Events:	13704

Total splicing  Junctions:	104927
Known Splicing Junctions:	97339
Partial Novel Splicing Junctions:	2519
Novel Splicing Junctions:	5069

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