Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/56e589829c5a223a59869eaffe5a5b/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/24c3b12655677e9ee22ffad85b4004/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/24c3b12655677e9ee22ffad85b4004/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/05e9e37ee3344725e12eb87bcbdf74/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 ...