[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_40C_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% (4823092) splicing reads. 205924 splicing junctions. 172626 known splicing junctions. 33298 novel splicing junctions.
sampling 10% (9646184) splicing reads. 242816 splicing junctions. 186783 known splicing junctions. 56033 novel splicing junctions.
sampling 15% (14469276) splicing reads. 268182 splicing junctions. 194386 known splicing junctions. 73796 novel splicing junctions.
sampling 20% (19292368) splicing reads. 287865 splicing junctions. 199455 known splicing junctions. 88410 novel splicing junctions.
sampling 25% (24115460) splicing reads. 304098 splicing junctions. 203150 known splicing junctions. 100948 novel splicing junctions.
sampling 30% (28938552) splicing reads. 317760 splicing junctions. 205964 known splicing junctions. 111796 novel splicing junctions.
sampling 35% (33761645) splicing reads. 329549 splicing junctions. 208293 known splicing junctions. 121256 novel splicing junctions.
sampling 40% (38584737) splicing reads. 339436 splicing junctions. 210168 known splicing junctions. 129268 novel splicing junctions.
sampling 45% (43407829) splicing reads. 348090 splicing junctions. 211753 known splicing junctions. 136337 novel splicing junctions.
sampling 50% (48230921) splicing reads. 355573 splicing junctions. 212998 known splicing junctions. 142575 novel splicing junctions.
sampling 55% (53054013) splicing reads. 362164 splicing junctions. 214063 known splicing junctions. 148101 novel splicing junctions.
sampling 60% (57877105) splicing reads. 367890 splicing junctions. 214951 known splicing junctions. 152939 novel splicing junctions.
sampling 65% (62700197) splicing reads. 372786 splicing junctions. 215760 known splicing junctions. 157026 novel splicing junctions.
sampling 70% (67523290) splicing reads. 377113 splicing junctions. 216432 known splicing junctions. 160681 novel splicing junctions.
sampling 75% (72346382) splicing reads. 380714 splicing junctions. 216975 known splicing junctions. 163739 novel splicing junctions.
sampling 80% (77169474) splicing reads. 383800 splicing junctions. 217435 known splicing junctions. 166365 novel splicing junctions.
sampling 85% (81992566) splicing reads. 386430 splicing junctions. 217794 known splicing junctions. 168636 novel splicing junctions.
sampling 90% (86815658) splicing reads. 388483 splicing junctions. 218103 known splicing junctions. 170380 novel splicing junctions.
sampling 95% (91638750) splicing reads. 390126 splicing junctions. 218353 known splicing junctions. 171773 novel splicing junctions.
sampling 100% (96461843) splicing reads. 391271 splicing junctions. 218528 known splicing junctions. 172743 novel splicing junctions.