[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. 93766 splicing junctions. 89411 known splicing junctions. 4355 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112753 splicing junctions. 104802 known splicing junctions. 7951 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123766 splicing junctions. 112609 known splicing junctions. 11157 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131544 splicing junctions. 117514 known splicing junctions. 14030 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137703 splicing junctions. 121184 known splicing junctions. 16519 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142783 splicing junctions. 123979 known splicing junctions. 18804 novel splicing junctions.
sampling 35% (3926092) splicing reads. 147209 splicing junctions. 126315 known splicing junctions. 20894 novel splicing junctions.
sampling 40% (4486963) splicing reads. 151020 splicing junctions. 128161 known splicing junctions. 22859 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154402 splicing junctions. 129794 known splicing junctions. 24608 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157308 splicing junctions. 131143 known splicing junctions. 26165 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160126 splicing junctions. 132435 known splicing junctions. 27691 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162595 splicing junctions. 133500 known splicing junctions. 29095 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164930 splicing junctions. 134535 known splicing junctions. 30395 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166934 splicing junctions. 135387 known splicing junctions. 31547 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168742 splicing junctions. 136158 known splicing junctions. 32584 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170486 splicing junctions. 136880 known splicing junctions. 33606 novel splicing junctions.
sampling 85% (9534796) splicing reads. 171991 splicing junctions. 137480 known splicing junctions. 34511 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173436 splicing junctions. 138044 known splicing junctions. 35392 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174695 splicing junctions. 138533 known splicing junctions. 36162 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.