[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_27C_3.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% (5045136) splicing reads. 211400 splicing junctions. 174595 known splicing junctions. 36805 novel splicing junctions.
sampling 10% (10090273) splicing reads. 249608 splicing junctions. 188688 known splicing junctions. 60920 novel splicing junctions.
sampling 15% (15135409) splicing reads. 275652 splicing junctions. 196082 known splicing junctions. 79570 novel splicing junctions.
sampling 20% (20180546) splicing reads. 295839 splicing junctions. 201011 known splicing junctions. 94828 novel splicing junctions.
sampling 25% (25225683) splicing reads. 312132 splicing junctions. 204558 known splicing junctions. 107574 novel splicing junctions.
sampling 30% (30270819) splicing reads. 325548 splicing junctions. 207174 known splicing junctions. 118374 novel splicing junctions.
sampling 35% (35315956) splicing reads. 336910 splicing junctions. 209289 known splicing junctions. 127621 novel splicing junctions.
sampling 40% (40361093) splicing reads. 346829 splicing junctions. 211058 known splicing junctions. 135771 novel splicing junctions.
sampling 45% (45406229) splicing reads. 355263 splicing junctions. 212459 known splicing junctions. 142804 novel splicing junctions.
sampling 50% (50451366) splicing reads. 362474 splicing junctions. 213640 known splicing junctions. 148834 novel splicing junctions.
sampling 55% (55496503) splicing reads. 368633 splicing junctions. 214606 known splicing junctions. 154027 novel splicing junctions.
sampling 60% (60541639) splicing reads. 374092 splicing junctions. 215471 known splicing junctions. 158621 novel splicing junctions.
sampling 65% (65586776) splicing reads. 378941 splicing junctions. 216196 known splicing junctions. 162745 novel splicing junctions.
sampling 70% (70631913) splicing reads. 383076 splicing junctions. 216764 known splicing junctions. 166312 novel splicing junctions.
sampling 75% (75677049) splicing reads. 386558 splicing junctions. 217255 known splicing junctions. 169303 novel splicing junctions.
sampling 80% (80722186) splicing reads. 389451 splicing junctions. 217689 known splicing junctions. 171762 novel splicing junctions.
sampling 85% (85767323) splicing reads. 391929 splicing junctions. 218054 known splicing junctions. 173875 novel splicing junctions.
sampling 90% (90812459) splicing reads. 393853 splicing junctions. 218351 known splicing junctions. 175502 novel splicing junctions.
sampling 95% (95857596) splicing reads. 395325 splicing junctions. 218584 known splicing junctions. 176741 novel splicing junctions.
sampling 100% (100902733) splicing reads. 396344 splicing junctions. 218731 known splicing junctions. 177613 novel splicing junctions.