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/93/ade26f870b48a7c42744c92608a5d6/.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/93/ade26f870b48a7c42744c92608a5d6/.command.run
==> STAGING COMPLETE (5 inputs)

[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! Total 386135 known splicing junctions.
Load BAM file ...  Done
shuffling alignments ... Done
sampling 5% (2128980) splicing reads. 120257 splicing junctions. 112727 known splicing junctions. 7530 novel splicing junctions.
sampling 10% (4257960) splicing reads. 128499 splicing junctions. 119096 known splicing junctions. 9403 novel splicing junctions.
sampling 15% (6386940) splicing reads. 132020 splicing junctions. 121484 known splicing junctions. 10536 novel splicing junctions.
sampling 20% (8515921) splicing reads. 134297 splicing junctions. 122846 known splicing junctions. 11451 novel splicing junctions.
sampling 25% (10644901) splicing reads. 135812 splicing junctions. 123672 known splicing junctions. 12140 novel splicing junctions.
sampling 30% (12773881) splicing reads. 136960 splicing junctions. 124262 known splicing junctions. 12698 novel splicing junctions.
sampling 35% (14902862) splicing reads. 137941 splicing junctions. 124721 known splicing junctions. 13220 novel splicing junctions.
sampling 40% (17031842) splicing reads. 138747 splicing junctions. 125083 known splicing junctions. 13664 novel splicing junctions.
sampling 45% (19160822) splicing reads. 139416 splicing junctions. 125370 known splicing junctions. 14046 novel splicing junctions.
sampling 50% (21289803) splicing reads. 139981 splicing junctions. 125613 known splicing junctions. 14368 novel splicing junctions.
sampling 55% (23418783) splicing reads. 140486 splicing junctions. 125804 known splicing junctions. 14682 novel splicing junctions.
sampling 60% (25547763) splicing reads. 140873 splicing junctions. 125958 known splicing junctions. 14915 novel splicing junctions.
sampling 65% (27676743) splicing reads. 141260 splicing junctions. 126107 known splicing junctions. 15153 novel splicing junctions.
sampling 70% (29805724) splicing reads. 141574 splicing junctions. 126228 known splicing junctions. 15346 novel splicing junctions.
sampling 75% (31934704) splicing reads. 141837 splicing junctions. 126317 known splicing junctions. 15520 novel splicing junctions.
sampling 80% (34063684) splicing reads. 142044 splicing junctions. 126391 known splicing junctions. 15653 novel splicing junctions.
sampling 85% (36192665) splicing reads. 142170 splicing junctions. 126441 known splicing junctions. 15729 novel splicing junctions.
sampling 90% (38321645) splicing reads. 142285 splicing junctions. 126481 known splicing junctions. 15804 novel splicing junctions.
sampling 95% (40450625) splicing reads. 142359 splicing junctions. 126503 known splicing junctions. 15856 novel splicing junctions.
sampling 100% (42579606) splicing reads. 142401 splicing junctions. 126519 known splicing junctions. 15882 novel splicing junctions.
null device 
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