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/f5/9ab5c4c62eed797fdf239e478f6da8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/9ab5c4c62eed797fdf239e478f6da8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/65f06cd3e9e66d1e34a7491dc5105b/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/e106d13faaf71d982b3721a6e6dcf1/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 28565037
[W::hts_idx_load3] The index file is older than the data file: BreastNB_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:	28565037
Known Splicing Events:	28255483
Partial Novel Splicing Events:	149220
Novel Splicing Events:	142663
Filtered Splicing Events:	17671

Total splicing  Junctions:	121846
Known Splicing Junctions:	111585
Partial Novel Splicing Junctions:	3735
Novel Splicing Junctions:	6526

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