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/cd/4d8574b708297e6d6d021c8cc08bfa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/e8e59ffccb205e8ca63548b7bc97ef/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/4d8574b708297e6d6d021c8cc08bfa/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/f2a5f29f2cf05d1cc4af6ddfb691f7/BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BT-20_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
reading reference bed file:  ref_annot.bed  ...  Done! Total 386135 known splicing junctions.
Load BAM file ...  Done
shuffling alignments ... Done
sampling 5% (1819478) splicing reads. 145898 splicing junctions. 132145 known splicing junctions. 13753 novel splicing junctions.
sampling 10% (3638957) splicing reads. 168084 splicing junctions. 146001 known splicing junctions. 22083 novel splicing junctions.
sampling 15% (5458436) splicing reads. 180572 splicing junctions. 152328 known splicing junctions. 28244 novel splicing junctions.
sampling 20% (7277915) splicing reads. 189038 splicing junctions. 156096 known splicing junctions. 32942 novel splicing junctions.
sampling 25% (9097394) splicing reads. 195548 splicing junctions. 158634 known splicing junctions. 36914 novel splicing junctions.
sampling 30% (10916873) splicing reads. 200600 splicing junctions. 160391 known splicing junctions. 40209 novel splicing junctions.
sampling 35% (12736351) splicing reads. 204787 splicing junctions. 161794 known splicing junctions. 42993 novel splicing junctions.
sampling 40% (14555830) splicing reads. 208219 splicing junctions. 162822 known splicing junctions. 45397 novel splicing junctions.
sampling 45% (16375309) splicing reads. 211145 splicing junctions. 163656 known splicing junctions. 47489 novel splicing junctions.
sampling 50% (18194788) splicing reads. 213729 splicing junctions. 164381 known splicing junctions. 49348 novel splicing junctions.
sampling 55% (20014267) splicing reads. 215873 splicing junctions. 164913 known splicing junctions. 50960 novel splicing junctions.
sampling 60% (21833746) splicing reads. 217718 splicing junctions. 165388 known splicing junctions. 52330 novel splicing junctions.
sampling 65% (23653225) splicing reads. 219263 splicing junctions. 165766 known splicing junctions. 53497 novel splicing junctions.
sampling 70% (25472703) splicing reads. 220585 splicing junctions. 166080 known splicing junctions. 54505 novel splicing junctions.
sampling 75% (27292182) splicing reads. 221636 splicing junctions. 166308 known splicing junctions. 55328 novel splicing junctions.
sampling 80% (29111661) splicing reads. 222454 splicing junctions. 166478 known splicing junctions. 55976 novel splicing junctions.
sampling 85% (30931140) splicing reads. 223149 splicing junctions. 166635 known splicing junctions. 56514 novel splicing junctions.
sampling 90% (32750619) splicing reads. 223630 splicing junctions. 166745 known splicing junctions. 56885 novel splicing junctions.
sampling 95% (34570098) splicing reads. 223962 splicing junctions. 166815 known splicing junctions. 57147 novel splicing junctions.
sampling 100% (36389577) splicing reads. 224079 splicing junctions. 166838 known splicing junctions. 57241 novel splicing junctions.
null device 
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