Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/ec3a10410562e6c89a0256d8bfdf6b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/aec77973b89d81529313915b9c4e31/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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/06/473a1d9e25d7676feaa10a020687b4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/473a1d9e25d7676feaa10a020687b4/.command.run
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 2878292
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	2878292
Known Splicing Events:	2801360
Partial Novel Splicing Events:	15144
Novel Splicing Events:	58002
Filtered Splicing Events:	3786

Total splicing  Junctions:	47633
Known Splicing Junctions:	45324
Partial Novel Splicing Junctions:	618
Novel Splicing Junctions:	1691

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