Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/3c8d62dc6d65d71fe07b3391a2e13d/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/b6bead23341fde9857211b1a793053/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/0b405e7195aed83c0db02fdfe02b84/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/fcdc578cb11e1b19e2a068ba3276d8/aih-tih-sc-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/b6bead23341fde9857211b1a793053/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-28eb14-R1_A23YTGFLT4_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% (16383657) splicing reads. 265273 splicing junctions. 186986 known splicing junctions. 78287 novel splicing junctions.
sampling 10% (32767314) splicing reads. 326149 splicing junctions. 200256 known splicing junctions. 125893 novel splicing junctions.
sampling 15% (49150971) splicing reads. 370332 splicing junctions. 207441 known splicing junctions. 162891 novel splicing junctions.
sampling 20% (65534628) splicing reads. 405538 splicing junctions. 212231 known splicing junctions. 193307 novel splicing junctions.
sampling 25% (81918285) splicing reads. 434883 splicing junctions. 215813 known splicing junctions. 219070 novel splicing junctions.
sampling 30% (98301942) splicing reads. 459987 splicing junctions. 218494 known splicing junctions. 241493 novel splicing junctions.
sampling 35% (114685599) splicing reads. 481870 splicing junctions. 220672 known splicing junctions. 261198 novel splicing junctions.
sampling 40% (131069256) splicing reads. 501231 splicing junctions. 222484 known splicing junctions. 278747 novel splicing junctions.
sampling 45% (147452913) splicing reads. 518336 splicing junctions. 223951 known splicing junctions. 294385 novel splicing junctions.
sampling 50% (163836570) splicing reads. 533578 splicing junctions. 225205 known splicing junctions. 308373 novel splicing junctions.
sampling 55% (180220227) splicing reads. 547215 splicing junctions. 226281 known splicing junctions. 320934 novel splicing junctions.
sampling 60% (196603884) splicing reads. 559206 splicing junctions. 227174 known splicing junctions. 332032 novel splicing junctions.
sampling 65% (212987541) splicing reads. 569979 splicing junctions. 228000 known splicing junctions. 341979 novel splicing junctions.
sampling 70% (229371198) splicing reads. 579574 splicing junctions. 228715 known splicing junctions. 350859 novel splicing junctions.
sampling 75% (245754855) splicing reads. 587997 splicing junctions. 229294 known splicing junctions. 358703 novel splicing junctions.
sampling 80% (262138512) splicing reads. 595399 splicing junctions. 229794 known splicing junctions. 365605 novel splicing junctions.
sampling 85% (278522169) splicing reads. 601854 splicing junctions. 230260 known splicing junctions. 371594 novel splicing junctions.
sampling 90% (294905826) splicing reads. 607399 splicing junctions. 230661 known splicing junctions. 376738 novel splicing junctions.
sampling 95% (311289483) splicing reads. 612089 splicing junctions. 230950 known splicing junctions. 381139 novel splicing junctions.
sampling 100% (327673140) splicing reads. 615961 splicing junctions. 231193 known splicing junctions. 384768 novel splicing junctions.
null device 
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