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/92/adb4ece70e538f61974cac3d4c727d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/adb4ece70e538f61974cac3d4c727d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/5ef34901cf4eadded45cac52de7e0c/659_bKP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/6a433b48423cb1b81bcb42ff22b6ec/659_bKP-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_bKP-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% (15839754) splicing reads. 266546 splicing junctions. 182668 known splicing junctions. 83878 novel splicing junctions.
sampling 10% (31679508) splicing reads. 327681 splicing junctions. 195156 known splicing junctions. 132525 novel splicing junctions.
sampling 15% (47519262) splicing reads. 370114 splicing junctions. 201704 known splicing junctions. 168410 novel splicing junctions.
sampling 20% (63359016) splicing reads. 402682 splicing junctions. 205911 known splicing junctions. 196771 novel splicing junctions.
sampling 25% (79198770) splicing reads. 428354 splicing junctions. 208899 known splicing junctions. 219455 novel splicing junctions.
sampling 30% (95038524) splicing reads. 449376 splicing junctions. 211170 known splicing junctions. 238206 novel splicing junctions.
sampling 35% (110878278) splicing reads. 466727 splicing junctions. 212898 known splicing junctions. 253829 novel splicing junctions.
sampling 40% (126718032) splicing reads. 481875 splicing junctions. 214365 known splicing junctions. 267510 novel splicing junctions.
sampling 45% (142557786) splicing reads. 494642 splicing junctions. 215496 known splicing junctions. 279146 novel splicing junctions.
sampling 50% (158397541) splicing reads. 505407 splicing junctions. 216411 known splicing junctions. 288996 novel splicing junctions.
sampling 55% (174237295) splicing reads. 514821 splicing junctions. 217237 known splicing junctions. 297584 novel splicing junctions.
sampling 60% (190077049) splicing reads. 522909 splicing junctions. 217896 known splicing junctions. 305013 novel splicing junctions.
sampling 65% (205916803) splicing reads. 529896 splicing junctions. 218490 known splicing junctions. 311406 novel splicing junctions.
sampling 70% (221756557) splicing reads. 535716 splicing junctions. 218951 known splicing junctions. 316765 novel splicing junctions.
sampling 75% (237596311) splicing reads. 540921 splicing junctions. 219333 known splicing junctions. 321588 novel splicing junctions.
sampling 80% (253436065) splicing reads. 545147 splicing junctions. 219638 known splicing junctions. 325509 novel splicing junctions.
sampling 85% (269275819) splicing reads. 548615 splicing junctions. 219879 known splicing junctions. 328736 novel splicing junctions.
sampling 90% (285115573) splicing reads. 551390 splicing junctions. 220090 known splicing junctions. 331300 novel splicing junctions.
sampling 95% (300955327) splicing reads. 553572 splicing junctions. 220253 known splicing junctions. 333319 novel splicing junctions.
sampling 100% (316795082) splicing reads. 555156 splicing junctions. 220369 known splicing junctions. 334787 novel splicing junctions.
null device 
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