[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. 93919 splicing junctions. 89532 known splicing junctions. 4387 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112724 splicing junctions. 104795 known splicing junctions. 7929 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123613 splicing junctions. 112456 known splicing junctions. 11157 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131354 splicing junctions. 117402 known splicing junctions. 13952 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137530 splicing junctions. 121138 known splicing junctions. 16392 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142524 splicing junctions. 123894 known splicing junctions. 18630 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146844 splicing junctions. 126133 known splicing junctions. 20711 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150751 splicing junctions. 128081 known splicing junctions. 22670 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154205 splicing junctions. 129752 known splicing junctions. 24453 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157280 splicing junctions. 131239 known splicing junctions. 26041 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160065 splicing junctions. 132458 known splicing junctions. 27607 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162548 splicing junctions. 133538 known splicing junctions. 29010 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164851 splicing junctions. 134531 known splicing junctions. 30320 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166945 splicing junctions. 135406 known splicing junctions. 31539 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168809 splicing junctions. 136176 known splicing junctions. 32633 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170530 splicing junctions. 136882 known splicing junctions. 33648 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172146 splicing junctions. 137569 known splicing junctions. 34577 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173483 splicing junctions. 138055 known splicing junctions. 35428 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174693 splicing junctions. 138557 known splicing junctions. 36136 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.