[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. 93884 splicing junctions. 89571 known splicing junctions. 4313 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112789 splicing junctions. 104891 known splicing junctions. 7898 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123624 splicing junctions. 112547 known splicing junctions. 11077 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131301 splicing junctions. 117454 known splicing junctions. 13847 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137476 splicing junctions. 121131 known splicing junctions. 16345 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142542 splicing junctions. 123933 known splicing junctions. 18609 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146982 splicing junctions. 126315 known splicing junctions. 20667 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150799 splicing junctions. 128244 known splicing junctions. 22555 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154289 splicing junctions. 129889 known splicing junctions. 24400 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157401 splicing junctions. 131353 known splicing junctions. 26048 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160134 splicing junctions. 132566 known splicing junctions. 27568 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162614 splicing junctions. 133645 known splicing junctions. 28969 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164864 splicing junctions. 134619 known splicing junctions. 30245 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166946 splicing junctions. 135524 known splicing junctions. 31422 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168777 splicing junctions. 136253 known splicing junctions. 32524 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170452 splicing junctions. 136928 known splicing junctions. 33524 novel splicing junctions.
sampling 85% (9534796) splicing reads. 171960 splicing junctions. 137530 known splicing junctions. 34430 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173385 splicing junctions. 138077 known splicing junctions. 35308 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174710 splicing junctions. 138575 known splicing junctions. 36135 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.