[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. 93922 splicing junctions. 89491 known splicing junctions. 4431 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112717 splicing junctions. 104770 known splicing junctions. 7947 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123474 splicing junctions. 112404 known splicing junctions. 11070 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131372 splicing junctions. 117408 known splicing junctions. 13964 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137491 splicing junctions. 121004 known splicing junctions. 16487 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142665 splicing junctions. 123907 known splicing junctions. 18758 novel splicing junctions.
sampling 35% (3926092) splicing reads. 147056 splicing junctions. 126179 known splicing junctions. 20877 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150897 splicing junctions. 128134 known splicing junctions. 22763 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154362 splicing junctions. 129820 known splicing junctions. 24542 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157489 splicing junctions. 131265 known splicing junctions. 26224 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160150 splicing junctions. 132489 known splicing junctions. 27661 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162689 splicing junctions. 133625 known splicing junctions. 29064 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164978 splicing junctions. 134629 known splicing junctions. 30349 novel splicing junctions.
sampling 70% (7852185) splicing reads. 167037 splicing junctions. 135510 known splicing junctions. 31527 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168965 splicing junctions. 136274 known splicing junctions. 32691 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170593 splicing junctions. 136917 known splicing junctions. 33676 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172119 splicing junctions. 137514 known splicing junctions. 34605 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173541 splicing junctions. 138087 known splicing junctions. 35454 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174747 splicing junctions. 138575 known splicing junctions. 36172 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.