Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ead7548c923424c68495c616845975/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/46a791ddfa811ce4947f367b6e37c7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/46a791ddfa811ce4947f367b6e37c7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/ede3b5bfad4a0d6517c7c51370e11b/659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/1e7a073df68f2c1a6261e2fd036c73/659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bR4-T1-TRNA-1_B23MHV2LT4_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% (14611633) splicing reads. 289829 splicing junctions. 197468 known splicing junctions. 92361 novel splicing junctions.
sampling 10% (29223266) splicing reads. 358675 splicing junctions. 210400 known splicing junctions. 148275 novel splicing junctions.
sampling 15% (43834899) splicing reads. 409620 splicing junctions. 217516 known splicing junctions. 192104 novel splicing junctions.
sampling 20% (58446533) splicing reads. 450475 splicing junctions. 222158 known splicing junctions. 228317 novel splicing junctions.
sampling 25% (73058166) splicing reads. 484460 splicing junctions. 225503 known splicing junctions. 258957 novel splicing junctions.
sampling 30% (87669799) splicing reads. 513873 splicing junctions. 228198 known splicing junctions. 285675 novel splicing junctions.
sampling 35% (102281432) splicing reads. 539289 splicing junctions. 230369 known splicing junctions. 308920 novel splicing junctions.
sampling 40% (116893066) splicing reads. 561759 splicing junctions. 232121 known splicing junctions. 329638 novel splicing junctions.
sampling 45% (131504699) splicing reads. 581613 splicing junctions. 233603 known splicing junctions. 348010 novel splicing junctions.
sampling 50% (146116332) splicing reads. 599164 splicing junctions. 234839 known splicing junctions. 364325 novel splicing junctions.
sampling 55% (160727965) splicing reads. 614864 splicing junctions. 235870 known splicing junctions. 378994 novel splicing junctions.
sampling 60% (175339599) splicing reads. 628703 splicing junctions. 236788 known splicing junctions. 391915 novel splicing junctions.
sampling 65% (189951232) splicing reads. 640996 splicing junctions. 237558 known splicing junctions. 403438 novel splicing junctions.
sampling 70% (204562865) splicing reads. 651839 splicing junctions. 238213 known splicing junctions. 413626 novel splicing junctions.
sampling 75% (219174498) splicing reads. 661486 splicing junctions. 238795 known splicing junctions. 422691 novel splicing junctions.
sampling 80% (233786132) splicing reads. 669784 splicing junctions. 239272 known splicing junctions. 430512 novel splicing junctions.
sampling 85% (248397765) splicing reads. 676978 splicing junctions. 239712 known splicing junctions. 437266 novel splicing junctions.
sampling 90% (263009398) splicing reads. 683139 splicing junctions. 240065 known splicing junctions. 443074 novel splicing junctions.
sampling 95% (277621031) splicing reads. 688315 splicing junctions. 240375 known splicing junctions. 447940 novel splicing junctions.
sampling 100% (292232665) splicing reads. 692380 splicing junctions. 240618 known splicing junctions. 451762 novel splicing junctions.
null device 
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