Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ebb8d66d0e4680eaed709c7ce41c82/BreastNP_FFPE_L02_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/ab/38c1c7f8650566a028f2c21ef16982/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/38c1c7f8650566a028f2c21ef16982/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d20a971c93be1dc46f16704254326/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 4142211
[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	4142211
Known Splicing Events:	4064461
Partial Novel Splicing Events:	25435
Novel Splicing Events:	49507
Filtered Splicing Events:	2808

Total splicing  Junctions:	99892
Known Splicing Junctions:	93921
Partial Novel Splicing Junctions:	2491
Novel Splicing Junctions:	3480

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