[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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% (143710) splicing reads. 32811 splicing junctions. 31697 known splicing junctions. 1114 novel splicing junctions.
sampling 10% (287421) splicing reads. 38790 splicing junctions. 37351 known splicing junctions. 1439 novel splicing junctions.
sampling 15% (431132) splicing reads. 41428 splicing junctions. 39774 known splicing junctions. 1654 novel splicing junctions.
sampling 20% (574843) splicing reads. 42958 splicing junctions. 41153 known splicing junctions. 1805 novel splicing junctions.
sampling 25% (718554) splicing reads. 43975 splicing junctions. 42058 known splicing junctions. 1917 novel splicing junctions.
sampling 30% (862265) splicing reads. 44708 splicing junctions. 42693 known splicing junctions. 2015 novel splicing junctions.
sampling 35% (1005975) splicing reads. 45276 splicing junctions. 43174 known splicing junctions. 2102 novel splicing junctions.
sampling 40% (1149686) splicing reads. 45733 splicing junctions. 43548 known splicing junctions. 2185 novel splicing junctions.
sampling 45% (1293397) splicing reads. 46087 splicing junctions. 43845 known splicing junctions. 2242 novel splicing junctions.
sampling 50% (1437108) splicing reads. 46391 splicing junctions. 44096 known splicing junctions. 2295 novel splicing junctions.
sampling 55% (1580819) splicing reads. 46667 splicing junctions. 44328 known splicing junctions. 2339 novel splicing junctions.
sampling 60% (1724530) splicing reads. 46879 splicing junctions. 44490 known splicing junctions. 2389 novel splicing junctions.
sampling 65% (1868241) splicing reads. 47066 splicing junctions. 44634 known splicing junctions. 2432 novel splicing junctions.
sampling 70% (2011951) splicing reads. 47201 splicing junctions. 44735 known splicing junctions. 2466 novel splicing junctions.
sampling 75% (2155662) splicing reads. 47321 splicing junctions. 44831 known splicing junctions. 2490 novel splicing junctions.
sampling 80% (2299373) splicing reads. 47422 splicing junctions. 44907 known splicing junctions. 2515 novel splicing junctions.
sampling 85% (2443084) splicing reads. 47494 splicing junctions. 44962 known splicing junctions. 2532 novel splicing junctions.
sampling 90% (2586795) splicing reads. 47543 splicing junctions. 45002 known splicing junctions. 2541 novel splicing junctions.
sampling 95% (2730506) splicing reads. 47573 splicing junctions. 45018 known splicing junctions. 2555 novel splicing junctions.
sampling 100% (2874217) splicing reads. 47585 splicing junctions. 45024 known splicing junctions. 2561 novel splicing junctions.