Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/ac8b1eaf7821ffd60f3b23b69cdca6/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  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/cd/e13f2f55ed0d5941a1ddfbfb8750e9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/e13f2f55ed0d5941a1ddfbfb8750e9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2019f56f93e4025d3ff4dd0e34946d/A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: A673_FFPE_RNA_0001_B23LG7FLT4_3.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% (15210281) splicing reads. 244441 splicing junctions. 167565 known splicing junctions. 76876 novel splicing junctions.
sampling 10% (30420562) splicing reads. 303905 splicing junctions. 180298 known splicing junctions. 123607 novel splicing junctions.
sampling 15% (45630844) splicing reads. 347495 splicing junctions. 187523 known splicing junctions. 159972 novel splicing junctions.
sampling 20% (60841125) splicing reads. 382140 splicing junctions. 192355 known splicing junctions. 189785 novel splicing junctions.
sampling 25% (76051407) splicing reads. 410947 splicing junctions. 195938 known splicing junctions. 215009 novel splicing junctions.
sampling 30% (91261688) splicing reads. 435332 splicing junctions. 198640 known splicing junctions. 236692 novel splicing junctions.
sampling 35% (106471969) splicing reads. 456547 splicing junctions. 200776 known splicing junctions. 255771 novel splicing junctions.
sampling 40% (121682251) splicing reads. 474941 splicing junctions. 202599 known splicing junctions. 272342 novel splicing junctions.
sampling 45% (136892532) splicing reads. 491151 splicing junctions. 204044 known splicing junctions. 287107 novel splicing junctions.
sampling 50% (152102814) splicing reads. 505481 splicing junctions. 205305 known splicing junctions. 300176 novel splicing junctions.
sampling 55% (167313095) splicing reads. 518278 splicing junctions. 206376 known splicing junctions. 311902 novel splicing junctions.
sampling 60% (182523376) splicing reads. 529577 splicing junctions. 207272 known splicing junctions. 322305 novel splicing junctions.
sampling 65% (197733658) splicing reads. 539694 splicing junctions. 208108 known splicing junctions. 331586 novel splicing junctions.
sampling 70% (212943939) splicing reads. 548556 splicing junctions. 208835 known splicing junctions. 339721 novel splicing junctions.
sampling 75% (228154221) splicing reads. 556283 splicing junctions. 209447 known splicing junctions. 346836 novel splicing junctions.
sampling 80% (243364502) splicing reads. 562799 splicing junctions. 209927 known splicing junctions. 352872 novel splicing junctions.
sampling 85% (258574783) splicing reads. 568544 splicing junctions. 210323 known splicing junctions. 358221 novel splicing junctions.
sampling 90% (273785065) splicing reads. 573231 splicing junctions. 210668 known splicing junctions. 362563 novel splicing junctions.
sampling 95% (288995346) splicing reads. 577113 splicing junctions. 210935 known splicing junctions. 366178 novel splicing junctions.
sampling 100% (304205628) splicing reads. 580103 splicing junctions. 211127 known splicing junctions. 368976 novel splicing junctions.
null device 
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