[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_40C_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% (4888084) splicing reads. 206613 splicing junctions. 173023 known splicing junctions. 33590 novel splicing junctions.
sampling 10% (9776169) splicing reads. 243490 splicing junctions. 187284 known splicing junctions. 56206 novel splicing junctions.
sampling 15% (14664253) splicing reads. 268913 splicing junctions. 194826 known splicing junctions. 74087 novel splicing junctions.
sampling 20% (19552338) splicing reads. 288693 splicing junctions. 199873 known splicing junctions. 88820 novel splicing junctions.
sampling 25% (24440422) splicing reads. 304752 splicing junctions. 203578 known splicing junctions. 101174 novel splicing junctions.
sampling 30% (29328507) splicing reads. 318221 splicing junctions. 206393 known splicing junctions. 111828 novel splicing junctions.
sampling 35% (34216591) splicing reads. 329472 splicing junctions. 208556 known splicing junctions. 120916 novel splicing junctions.
sampling 40% (39104676) splicing reads. 339181 splicing junctions. 210263 known splicing junctions. 128918 novel splicing junctions.
sampling 45% (43992760) splicing reads. 347534 splicing junctions. 211741 known splicing junctions. 135793 novel splicing junctions.
sampling 50% (48880845) splicing reads. 355003 splicing junctions. 212974 known splicing junctions. 142029 novel splicing junctions.
sampling 55% (53768930) splicing reads. 361532 splicing junctions. 214031 known splicing junctions. 147501 novel splicing junctions.
sampling 60% (58657014) splicing reads. 367042 splicing junctions. 214960 known splicing junctions. 152082 novel splicing junctions.
sampling 65% (63545099) splicing reads. 371969 splicing junctions. 215702 known splicing junctions. 156267 novel splicing junctions.
sampling 70% (68433183) splicing reads. 376213 splicing junctions. 216345 known splicing junctions. 159868 novel splicing junctions.
sampling 75% (73321268) splicing reads. 379859 splicing junctions. 216880 known splicing junctions. 162979 novel splicing junctions.
sampling 80% (78209352) splicing reads. 382895 splicing junctions. 217314 known splicing junctions. 165581 novel splicing junctions.
sampling 85% (83097437) splicing reads. 385466 splicing junctions. 217718 known splicing junctions. 167748 novel splicing junctions.
sampling 90% (87985521) splicing reads. 387458 splicing junctions. 217981 known splicing junctions. 169477 novel splicing junctions.
sampling 95% (92873606) splicing reads. 388981 splicing junctions. 218208 known splicing junctions. 170773 novel splicing junctions.
sampling 100% (97761691) splicing reads. 390113 splicing junctions. 218390 known splicing junctions. 171723 novel splicing junctions.