[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. 94066 splicing junctions. 89708 known splicing junctions. 4358 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112771 splicing junctions. 104823 known splicing junctions. 7948 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123617 splicing junctions. 112529 known splicing junctions. 11088 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131183 splicing junctions. 117369 known splicing junctions. 13814 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137307 splicing junctions. 121028 known splicing junctions. 16279 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142360 splicing junctions. 123836 known splicing junctions. 18524 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146786 splicing junctions. 126169 known splicing junctions. 20617 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150645 splicing junctions. 128076 known splicing junctions. 22569 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154155 splicing junctions. 129773 known splicing junctions. 24382 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157159 splicing junctions. 131159 known splicing junctions. 26000 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160000 splicing junctions. 132435 known splicing junctions. 27565 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162535 splicing junctions. 133551 known splicing junctions. 28984 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164831 splicing junctions. 134545 known splicing junctions. 30286 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166959 splicing junctions. 135426 known splicing junctions. 31533 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168786 splicing junctions. 136182 known splicing junctions. 32604 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170508 splicing junctions. 136879 known splicing junctions. 33629 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172084 splicing junctions. 137475 known splicing junctions. 34609 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173422 splicing junctions. 138028 known splicing junctions. 35394 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174670 splicing junctions. 138547 known splicing junctions. 36123 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.