[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_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% (856730) splicing reads. 81688 splicing junctions. 78509 known splicing junctions. 3179 novel splicing junctions.
sampling 10% (1713460) splicing reads. 89994 splicing junctions. 85952 known splicing junctions. 4042 novel splicing junctions.
sampling 15% (2570190) splicing reads. 93277 splicing junctions. 88766 known splicing junctions. 4511 novel splicing junctions.
sampling 20% (3426920) splicing reads. 95047 splicing junctions. 90192 known splicing junctions. 4855 novel splicing junctions.
sampling 25% (4283650) splicing reads. 96261 splicing junctions. 91147 known splicing junctions. 5114 novel splicing junctions.
sampling 30% (5140380) splicing reads. 97219 splicing junctions. 91852 known splicing junctions. 5367 novel splicing junctions.
sampling 35% (5997110) splicing reads. 97900 splicing junctions. 92351 known splicing junctions. 5549 novel splicing junctions.
sampling 40% (6853840) splicing reads. 98474 splicing junctions. 92761 known splicing junctions. 5713 novel splicing junctions.
sampling 45% (7710570) splicing reads. 98955 splicing junctions. 93100 known splicing junctions. 5855 novel splicing junctions.
sampling 50% (8567301) splicing reads. 99314 splicing junctions. 93343 known splicing junctions. 5971 novel splicing junctions.
sampling 55% (9424031) splicing reads. 99615 splicing junctions. 93555 known splicing junctions. 6060 novel splicing junctions.
sampling 60% (10280761) splicing reads. 99884 splicing junctions. 93712 known splicing junctions. 6172 novel splicing junctions.
sampling 65% (11137491) splicing reads. 100130 splicing junctions. 93870 known splicing junctions. 6260 novel splicing junctions.
sampling 70% (11994221) splicing reads. 100337 splicing junctions. 94000 known splicing junctions. 6337 novel splicing junctions.
sampling 75% (12850951) splicing reads. 100505 splicing junctions. 94111 known splicing junctions. 6394 novel splicing junctions.
sampling 80% (13707681) splicing reads. 100635 splicing junctions. 94190 known splicing junctions. 6445 novel splicing junctions.
sampling 85% (14564411) splicing reads. 100728 splicing junctions. 94240 known splicing junctions. 6488 novel splicing junctions.
sampling 90% (15421141) splicing reads. 100809 splicing junctions. 94280 known splicing junctions. 6529 novel splicing junctions.
sampling 95% (16277871) splicing reads. 100858 splicing junctions. 94311 known splicing junctions. 6547 novel splicing junctions.
sampling 100% (17134602) splicing reads. 100883 splicing junctions. 94328 known splicing junctions. 6555 novel splicing junctions.