Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/faf713aa7f9b598e8a66046a6c5c9c/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/ca4d20e41802bc8c33ea65523f74cb/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c99535b938d65f3b53fdf5e5a85503/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/c99535b938d65f3b53fdf5e5a85503/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/2060de38ad44935437caedd78a2177/1173_CI9_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 1173_CI9_T1_RNA_SLD_01_A23T55JLT4_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% (8660591) splicing reads. 215888 splicing junctions. 172461 known splicing junctions. 43427 novel splicing junctions.
sampling 10% (17321183) splicing reads. 253981 splicing junctions. 185231 known splicing junctions. 68750 novel splicing junctions.
sampling 15% (25981775) splicing reads. 280029 splicing junctions. 192304 known splicing junctions. 87725 novel splicing junctions.
sampling 20% (34642366) splicing reads. 299868 splicing junctions. 196989 known splicing junctions. 102879 novel splicing junctions.
sampling 25% (43302958) splicing reads. 315828 splicing junctions. 200297 known splicing junctions. 115531 novel splicing junctions.
sampling 30% (51963550) splicing reads. 328908 splicing junctions. 202842 known splicing junctions. 126066 novel splicing junctions.
sampling 35% (60624141) splicing reads. 340151 splicing junctions. 204851 known splicing junctions. 135300 novel splicing junctions.
sampling 40% (69284733) splicing reads. 349433 splicing junctions. 206410 known splicing junctions. 143023 novel splicing junctions.
sampling 45% (77945325) splicing reads. 357557 splicing junctions. 207765 known splicing junctions. 149792 novel splicing junctions.
sampling 50% (86605917) splicing reads. 364679 splicing junctions. 208940 known splicing junctions. 155739 novel splicing junctions.
sampling 55% (95266508) splicing reads. 370629 splicing junctions. 209907 known splicing junctions. 160722 novel splicing junctions.
sampling 60% (103927100) splicing reads. 375782 splicing junctions. 210691 known splicing junctions. 165091 novel splicing junctions.
sampling 65% (112587692) splicing reads. 380181 splicing junctions. 211363 known splicing junctions. 168818 novel splicing junctions.
sampling 70% (121248283) splicing reads. 383886 splicing junctions. 211903 known splicing junctions. 171983 novel splicing junctions.
sampling 75% (129908875) splicing reads. 386963 splicing junctions. 212351 known splicing junctions. 174612 novel splicing junctions.
sampling 80% (138569467) splicing reads. 389518 splicing junctions. 212714 known splicing junctions. 176804 novel splicing junctions.
sampling 85% (147230058) splicing reads. 391582 splicing junctions. 213031 known splicing junctions. 178551 novel splicing junctions.
sampling 90% (155890650) splicing reads. 393117 splicing junctions. 213255 known splicing junctions. 179862 novel splicing junctions.
sampling 95% (164551242) splicing reads. 394191 splicing junctions. 213415 known splicing junctions. 180776 novel splicing junctions.
sampling 100% (173211834) splicing reads. 394875 splicing junctions. 213510 known splicing junctions. 181365 novel splicing junctions.
null device 
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