Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f789d11d3dfd58975ba1c1dd754edc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/3f5ec9f0a169d4d484b81b4e99fa4e/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/c7b68403924fe7d1929c6897e4188e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/c7b68403924fe7d1929c6897e4188e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/71117a58f0b32aa82ed8ea882f6136/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_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% (836163) splicing reads. 82960 splicing junctions. 79561 known splicing junctions. 3399 novel splicing junctions.
sampling 10% (1672326) splicing reads. 91873 splicing junctions. 87409 known splicing junctions. 4464 novel splicing junctions.
sampling 15% (2508489) splicing reads. 95574 splicing junctions. 90438 known splicing junctions. 5136 novel splicing junctions.
sampling 20% (3344652) splicing reads. 97708 splicing junctions. 92056 known splicing junctions. 5652 novel splicing junctions.
sampling 25% (4180815) splicing reads. 99164 splicing junctions. 93087 known splicing junctions. 6077 novel splicing junctions.
sampling 30% (5016978) splicing reads. 100233 splicing junctions. 93770 known splicing junctions. 6463 novel splicing junctions.
sampling 35% (5853141) splicing reads. 101109 splicing junctions. 94319 known splicing junctions. 6790 novel splicing junctions.
sampling 40% (6689304) splicing reads. 101822 splicing junctions. 94746 known splicing junctions. 7076 novel splicing junctions.
sampling 45% (7525467) splicing reads. 102405 splicing junctions. 95080 known splicing junctions. 7325 novel splicing junctions.
sampling 50% (8361631) splicing reads. 102870 splicing junctions. 95336 known splicing junctions. 7534 novel splicing junctions.
sampling 55% (9197794) splicing reads. 103288 splicing junctions. 95550 known splicing junctions. 7738 novel splicing junctions.
sampling 60% (10033957) splicing reads. 103635 splicing junctions. 95743 known splicing junctions. 7892 novel splicing junctions.
sampling 65% (10870120) splicing reads. 103884 splicing junctions. 95875 known splicing junctions. 8009 novel splicing junctions.
sampling 70% (11706283) splicing reads. 104149 splicing junctions. 96020 known splicing junctions. 8129 novel splicing junctions.
sampling 75% (12542446) splicing reads. 104342 splicing junctions. 96101 known splicing junctions. 8241 novel splicing junctions.
sampling 80% (13378609) splicing reads. 104504 splicing junctions. 96185 known splicing junctions. 8319 novel splicing junctions.
sampling 85% (14214772) splicing reads. 104622 splicing junctions. 96243 known splicing junctions. 8379 novel splicing junctions.
sampling 90% (15050935) splicing reads. 104711 splicing junctions. 96278 known splicing junctions. 8433 novel splicing junctions.
sampling 95% (15887098) splicing reads. 104772 splicing junctions. 96311 known splicing junctions. 8461 novel splicing junctions.
sampling 100% (16723262) splicing reads. 104799 splicing junctions. 96326 known splicing junctions. 8473 novel splicing junctions.
null device 
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