Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/6b8ed2af8db4aec0135c02d1be12b3/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/6753bfb1d5115b29e8c6eb78327d1c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/6753bfb1d5115b29e8c6eb78327d1c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/3e8a82e76bbc12a902ec65f52defc1/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. 82910 splicing junctions. 79550 known splicing junctions. 3360 novel splicing junctions.
sampling 10% (1672326) splicing reads. 92065 splicing junctions. 87563 known splicing junctions. 4502 novel splicing junctions.
sampling 15% (2508489) splicing reads. 95750 splicing junctions. 90515 known splicing junctions. 5235 novel splicing junctions.
sampling 20% (3344652) splicing reads. 97867 splicing junctions. 92107 known splicing junctions. 5760 novel splicing junctions.
sampling 25% (4180815) splicing reads. 99315 splicing junctions. 93140 known splicing junctions. 6175 novel splicing junctions.
sampling 30% (5016978) splicing reads. 100323 splicing junctions. 93812 known splicing junctions. 6511 novel splicing junctions.
sampling 35% (5853141) splicing reads. 101190 splicing junctions. 94355 known splicing junctions. 6835 novel splicing junctions.
sampling 40% (6689304) splicing reads. 101881 splicing junctions. 94762 known splicing junctions. 7119 novel splicing junctions.
sampling 45% (7525467) splicing reads. 102472 splicing junctions. 95101 known splicing junctions. 7371 novel splicing junctions.
sampling 50% (8361631) splicing reads. 102925 splicing junctions. 95351 known splicing junctions. 7574 novel splicing junctions.
sampling 55% (9197794) splicing reads. 103278 splicing junctions. 95542 known splicing junctions. 7736 novel splicing junctions.
sampling 60% (10033957) splicing reads. 103611 splicing junctions. 95721 known splicing junctions. 7890 novel splicing junctions.
sampling 65% (10870120) splicing reads. 103903 splicing junctions. 95884 known splicing junctions. 8019 novel splicing junctions.
sampling 70% (11706283) splicing reads. 104140 splicing junctions. 96003 known splicing junctions. 8137 novel splicing junctions.
sampling 75% (12542446) splicing reads. 104350 splicing junctions. 96098 known splicing junctions. 8252 novel splicing junctions.
sampling 80% (13378609) splicing reads. 104502 splicing junctions. 96174 known splicing junctions. 8328 novel splicing junctions.
sampling 85% (14214772) splicing reads. 104623 splicing junctions. 96237 known splicing junctions. 8386 novel splicing junctions.
sampling 90% (15050935) splicing reads. 104709 splicing junctions. 96277 known splicing junctions. 8432 novel splicing junctions.
sampling 95% (15887098) splicing reads. 104773 splicing junctions. 96312 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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