[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% (560912) splicing reads. 93997 splicing junctions. 89663 known splicing junctions. 4334 novel splicing junctions.
sampling 10% (1121824) splicing reads. 112730 splicing junctions. 104788 known splicing junctions. 7942 novel splicing junctions.
sampling 15% (1682736) splicing reads. 123611 splicing junctions. 112422 known splicing junctions. 11189 novel splicing junctions.
sampling 20% (2243649) splicing reads. 131383 splicing junctions. 117361 known splicing junctions. 14022 novel splicing junctions.
sampling 25% (2804561) splicing reads. 137495 splicing junctions. 120939 known splicing junctions. 16556 novel splicing junctions.
sampling 30% (3365473) splicing reads. 142657 splicing junctions. 123777 known splicing junctions. 18880 novel splicing junctions.
sampling 35% (3926385) splicing reads. 147034 splicing junctions. 126086 known splicing junctions. 20948 novel splicing junctions.
sampling 40% (4487298) splicing reads. 150934 splicing junctions. 128110 known splicing junctions. 22824 novel splicing junctions.
sampling 45% (5048210) splicing reads. 154341 splicing junctions. 129744 known splicing junctions. 24597 novel splicing junctions.
sampling 50% (5609122) splicing reads. 157513 splicing junctions. 131226 known splicing junctions. 26287 novel splicing junctions.
sampling 55% (6170034) splicing reads. 160376 splicing junctions. 132552 known splicing junctions. 27824 novel splicing junctions.
sampling 60% (6730947) splicing reads. 162895 splicing junctions. 133688 known splicing junctions. 29207 novel splicing junctions.
sampling 65% (7291859) splicing reads. 165239 splicing junctions. 134713 known splicing junctions. 30526 novel splicing junctions.
sampling 70% (7852771) splicing reads. 167283 splicing junctions. 135556 known splicing junctions. 31727 novel splicing junctions.
sampling 75% (8413683) splicing reads. 169150 splicing junctions. 136341 known splicing junctions. 32809 novel splicing junctions.
sampling 80% (8974596) splicing reads. 170856 splicing junctions. 137005 known splicing junctions. 33851 novel splicing junctions.
sampling 85% (9535508) splicing reads. 172345 splicing junctions. 137609 known splicing junctions. 34736 novel splicing junctions.
sampling 90% (10096420) splicing reads. 173722 splicing junctions. 138115 known splicing junctions. 35607 novel splicing junctions.
sampling 95% (10657332) splicing reads. 175052 splicing junctions. 138634 known splicing junctions. 36418 novel splicing junctions.
sampling 100% (11218245) splicing reads. 176197 splicing junctions. 139062 known splicing junctions. 37135 novel splicing junctions.