[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. 94197 splicing junctions. 89801 known splicing junctions. 4396 novel splicing junctions.
sampling 10% (1121740) splicing reads. 113061 splicing junctions. 105038 known splicing junctions. 8023 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123725 splicing junctions. 112646 known splicing junctions. 11079 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131307 splicing junctions. 117526 known splicing junctions. 13781 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137398 splicing junctions. 121148 known splicing junctions. 16250 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142516 splicing junctions. 123966 known splicing junctions. 18550 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146868 splicing junctions. 126205 known splicing junctions. 20663 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150895 splicing junctions. 128209 known splicing junctions. 22686 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154265 splicing junctions. 129831 known splicing junctions. 24434 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157383 splicing junctions. 131265 known splicing junctions. 26118 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160076 splicing junctions. 132503 known splicing junctions. 27573 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162627 splicing junctions. 133603 known splicing junctions. 29024 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164936 splicing junctions. 134580 known splicing junctions. 30356 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166937 splicing junctions. 135456 known splicing junctions. 31481 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168844 splicing junctions. 136236 known splicing junctions. 32608 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170547 splicing junctions. 136948 known splicing junctions. 33599 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172019 splicing junctions. 137549 known splicing junctions. 34470 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173501 splicing junctions. 138117 known splicing junctions. 35384 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174755 splicing junctions. 138586 known splicing junctions. 36169 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.