[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.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% (560870) splicing reads. 94011 splicing junctions. 89578 known splicing junctions. 4433 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112755 splicing junctions. 104779 known splicing junctions. 7976 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123627 splicing junctions. 112474 known splicing junctions. 11153 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131275 splicing junctions. 117347 known splicing junctions. 13928 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137608 splicing junctions. 121065 known splicing junctions. 16543 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142539 splicing junctions. 123790 known splicing junctions. 18749 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146921 splicing junctions. 126097 known splicing junctions. 20824 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150694 splicing junctions. 128004 known splicing junctions. 22690 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154172 splicing junctions. 129633 known splicing junctions. 24539 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157261 splicing junctions. 131089 known splicing junctions. 26172 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160001 splicing junctions. 132360 known splicing junctions. 27641 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162461 splicing junctions. 133465 known splicing junctions. 28996 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164763 splicing junctions. 134478 known splicing junctions. 30285 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166814 splicing junctions. 135338 known splicing junctions. 31476 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168721 splicing junctions. 136158 known splicing junctions. 32563 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170442 splicing junctions. 136857 known splicing junctions. 33585 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172029 splicing junctions. 137522 known splicing junctions. 34507 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173418 splicing junctions. 138082 known splicing junctions. 35336 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174662 splicing junctions. 138563 known splicing junctions. 36099 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.