Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/04c4c44ea17fe7421b72d5f28c777c/659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/b02a7396bf6caf366aae276126d7b9/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c7895d2806582b5335f7e4b905a7f8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c7895d2806582b5335f7e4b905a7f8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/596dc83cd135ae3e53e2e69434618e/659_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_cfy-T1-TRNA-1_B23WHTKLT4_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% (18066809) splicing reads. 260614 splicing junctions. 183855 known splicing junctions. 76759 novel splicing junctions.
sampling 10% (36133619) splicing reads. 315016 splicing junctions. 195474 known splicing junctions. 119542 novel splicing junctions.
sampling 15% (54200429) splicing reads. 350788 splicing junctions. 201340 known splicing junctions. 149448 novel splicing junctions.
sampling 20% (72267239) splicing reads. 376963 splicing junctions. 205030 known splicing junctions. 171933 novel splicing junctions.
sampling 25% (90334049) splicing reads. 397047 splicing junctions. 207589 known splicing junctions. 189458 novel splicing junctions.
sampling 30% (108400859) splicing reads. 412811 splicing junctions. 209400 known splicing junctions. 203411 novel splicing junctions.
sampling 35% (126467668) splicing reads. 425670 splicing junctions. 210854 known splicing junctions. 214816 novel splicing junctions.
sampling 40% (144534478) splicing reads. 436040 splicing junctions. 211976 known splicing junctions. 224064 novel splicing junctions.
sampling 45% (162601288) splicing reads. 444873 splicing junctions. 212905 known splicing junctions. 231968 novel splicing junctions.
sampling 50% (180668098) splicing reads. 452244 splicing junctions. 213653 known splicing junctions. 238591 novel splicing junctions.
sampling 55% (198734908) splicing reads. 458611 splicing junctions. 214263 known splicing junctions. 244348 novel splicing junctions.
sampling 60% (216801718) splicing reads. 463932 splicing junctions. 214741 known splicing junctions. 249191 novel splicing junctions.
sampling 65% (234868528) splicing reads. 468476 splicing junctions. 215162 known splicing junctions. 253314 novel splicing junctions.
sampling 70% (252935337) splicing reads. 472556 splicing junctions. 215550 known splicing junctions. 257006 novel splicing junctions.
sampling 75% (271002147) splicing reads. 475983 splicing junctions. 215847 known splicing junctions. 260136 novel splicing junctions.
sampling 80% (289068957) splicing reads. 478945 splicing junctions. 216113 known splicing junctions. 262832 novel splicing junctions.
sampling 85% (307135767) splicing reads. 481409 splicing junctions. 216300 known splicing junctions. 265109 novel splicing junctions.
sampling 90% (325202577) splicing reads. 483404 splicing junctions. 216464 known splicing junctions. 266940 novel splicing junctions.
sampling 95% (343269387) splicing reads. 485012 splicing junctions. 216603 known splicing junctions. 268409 novel splicing junctions.
sampling 100% (361336197) splicing reads. 486345 splicing junctions. 216722 known splicing junctions. 269623 novel splicing junctions.
null device 
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