Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/88a81337442ba432134f1623a5dda6/659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/340e30ce4f4dec54a95b5e1de8b372/659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/f73a0e22861201cc7c5cccf07ed1b4/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/6bb714e56f0130b809064f7ff3330a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/6bb714e56f0130b809064f7ff3330a/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_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% (16663738) splicing reads. 282477 splicing junctions. 193573 known splicing junctions. 88904 novel splicing junctions.
sampling 10% (33327477) splicing reads. 344450 splicing junctions. 205594 known splicing junctions. 138856 novel splicing junctions.
sampling 15% (49991216) splicing reads. 387124 splicing junctions. 211860 known splicing junctions. 175264 novel splicing junctions.
sampling 20% (66654954) splicing reads. 419387 splicing junctions. 215800 known splicing junctions. 203587 novel splicing junctions.
sampling 25% (83318693) splicing reads. 444823 splicing junctions. 218603 known splicing junctions. 226220 novel splicing junctions.
sampling 30% (99982432) splicing reads. 465751 splicing junctions. 220710 known splicing junctions. 245041 novel splicing junctions.
sampling 35% (116646170) splicing reads. 482985 splicing junctions. 222418 known splicing junctions. 260567 novel splicing junctions.
sampling 40% (133309909) splicing reads. 497731 splicing junctions. 223667 known splicing junctions. 274064 novel splicing junctions.
sampling 45% (149973648) splicing reads. 510287 splicing junctions. 224779 known splicing junctions. 285508 novel splicing junctions.
sampling 50% (166637387) splicing reads. 520919 splicing junctions. 225637 known splicing junctions. 295282 novel splicing junctions.
sampling 55% (183301125) splicing reads. 530162 splicing junctions. 226369 known splicing junctions. 303793 novel splicing junctions.
sampling 60% (199964864) splicing reads. 537943 splicing junctions. 227005 known splicing junctions. 310938 novel splicing junctions.
sampling 65% (216628603) splicing reads. 544781 splicing junctions. 227529 known splicing junctions. 317252 novel splicing junctions.
sampling 70% (233292341) splicing reads. 550806 splicing junctions. 227971 known splicing junctions. 322835 novel splicing junctions.
sampling 75% (249956080) splicing reads. 555888 splicing junctions. 228331 known splicing junctions. 327557 novel splicing junctions.
sampling 80% (266619819) splicing reads. 560213 splicing junctions. 228635 known splicing junctions. 331578 novel splicing junctions.
sampling 85% (283283557) splicing reads. 563889 splicing junctions. 228904 known splicing junctions. 334985 novel splicing junctions.
sampling 90% (299947296) splicing reads. 566901 splicing junctions. 229120 known splicing junctions. 337781 novel splicing junctions.
sampling 95% (316611035) splicing reads. 569304 splicing junctions. 229302 known splicing junctions. 340002 novel splicing junctions.
sampling 100% (333274774) splicing reads. 571135 splicing junctions. 229439 known splicing junctions. 341696 novel splicing junctions.
null device 
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