Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/6754a97c6bbb3102a744d1eb4bd65f/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/c50e02f5baf80760d8092c2b427a64/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  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/99/e664418a8ab08bfb7ae686d598f2a4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/e664418a8ab08bfb7ae686d598f2a4/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-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% (14497421) splicing reads. 266157 splicing junctions. 190080 known splicing junctions. 76077 novel splicing junctions.
sampling 10% (28994842) splicing reads. 325476 splicing junctions. 202653 known splicing junctions. 122823 novel splicing junctions.
sampling 15% (43492263) splicing reads. 368535 splicing junctions. 209528 known splicing junctions. 159007 novel splicing junctions.
sampling 20% (57989684) splicing reads. 402192 splicing junctions. 214134 known splicing junctions. 188058 novel splicing junctions.
sampling 25% (72487105) splicing reads. 429865 splicing junctions. 217393 known splicing junctions. 212472 novel splicing junctions.
sampling 30% (86984526) splicing reads. 453651 splicing junctions. 219963 known splicing junctions. 233688 novel splicing junctions.
sampling 35% (101481947) splicing reads. 474152 splicing junctions. 222043 known splicing junctions. 252109 novel splicing junctions.
sampling 40% (115979368) splicing reads. 491759 splicing junctions. 223701 known splicing junctions. 268058 novel splicing junctions.
sampling 45% (130476789) splicing reads. 507053 splicing junctions. 225061 known splicing junctions. 281992 novel splicing junctions.
sampling 50% (144974210) splicing reads. 520611 splicing junctions. 226202 known splicing junctions. 294409 novel splicing junctions.
sampling 55% (159471631) splicing reads. 532536 splicing junctions. 227172 known splicing junctions. 305364 novel splicing junctions.
sampling 60% (173969052) splicing reads. 543125 splicing junctions. 228053 known splicing junctions. 315072 novel splicing junctions.
sampling 65% (188466473) splicing reads. 552089 splicing junctions. 228790 known splicing junctions. 323299 novel splicing junctions.
sampling 70% (202963894) splicing reads. 560041 splicing junctions. 229402 known splicing junctions. 330639 novel splicing junctions.
sampling 75% (217461315) splicing reads. 566999 splicing junctions. 229916 known splicing junctions. 337083 novel splicing junctions.
sampling 80% (231958736) splicing reads. 572940 splicing junctions. 230332 known splicing junctions. 342608 novel splicing junctions.
sampling 85% (246456157) splicing reads. 577986 splicing junctions. 230668 known splicing junctions. 347318 novel splicing junctions.
sampling 90% (260953578) splicing reads. 582184 splicing junctions. 230984 known splicing junctions. 351200 novel splicing junctions.
sampling 95% (275450999) splicing reads. 585513 splicing junctions. 231241 known splicing junctions. 354272 novel splicing junctions.
sampling 100% (289948421) splicing reads. 588125 splicing junctions. 231421 known splicing junctions. 356704 novel splicing junctions.
null device 
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