Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/976a206c506e2bfc1dcdbe9906f9f4/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.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/58/1fd8ae337ae9ee3892f8316699636f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/1fd8ae337ae9ee3892f8316699636f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/865b5c1e28a21171d2f43a3719ea8a/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

null device 
          1 
null device 
          1 
total = 6794754
[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Reading reference bed file:  ref_annot.bed  ...  Done
Load BAM file ...  Done

===================================================================
Total splicing  Events:	6794754
Known Splicing Events:	6664553
Partial Novel Splicing Events:	44844
Novel Splicing Events:	80103
Filtered Splicing Events:	5254

Total splicing  Junctions:	129832
Known Splicing Junctions:	120129
Partial Novel Splicing Junctions:	4565
Novel Splicing Junctions:	5138

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