Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/f7c46891ee12480c88775c01ab5059/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  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/48/780a561e506ecb884e9285d7b12899/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/2d6062a1134f981f2bd2faba13d16d/BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/780a561e506ecb884e9285d7b12899/.command.run
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 42612552
[W::hts_idx_load3] The index file is older than the data file: BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	42612552
Known Splicing Events:	42127037
Partial Novel Splicing Events:	239674
Novel Splicing Events:	215735
Filtered Splicing Events:	30106

Total splicing  Junctions:	142566
Known Splicing Junctions:	128692
Partial Novel Splicing Junctions:	5526
Novel Splicing Junctions:	8348

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