[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. 94074 splicing junctions. 89637 known splicing junctions. 4437 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112845 splicing junctions. 104907 known splicing junctions. 7938 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123678 splicing junctions. 112481 known splicing junctions. 11197 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131314 splicing junctions. 117377 known splicing junctions. 13937 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137357 splicing junctions. 120980 known splicing junctions. 16377 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142561 splicing junctions. 123880 known splicing junctions. 18681 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146985 splicing junctions. 126197 known splicing junctions. 20788 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150841 splicing junctions. 128157 known splicing junctions. 22684 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154310 splicing junctions. 129752 known splicing junctions. 24558 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157372 splicing junctions. 131211 known splicing junctions. 26161 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160073 splicing junctions. 132480 known splicing junctions. 27593 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162601 splicing junctions. 133587 known splicing junctions. 29014 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164822 splicing junctions. 134565 known splicing junctions. 30257 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166944 splicing junctions. 135454 known splicing junctions. 31490 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168815 splicing junctions. 136208 known splicing junctions. 32607 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170604 splicing junctions. 136974 known splicing junctions. 33630 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172146 splicing junctions. 137566 known splicing junctions. 34580 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173516 splicing junctions. 138099 known splicing junctions. 35417 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174697 splicing junctions. 138559 known splicing junctions. 36138 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.