[W::hts_idx_load3] The index file is older than the data file: dna_s739.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% (1099) splicing reads. 804 splicing junctions. 366 known splicing junctions. 438 novel splicing junctions.
sampling 10% (2199) splicing reads. 1342 splicing junctions. 548 known splicing junctions. 794 novel splicing junctions.
sampling 15% (3298) splicing reads. 1768 splicing junctions. 674 known splicing junctions. 1094 novel splicing junctions.
sampling 20% (4398) splicing reads. 2106 splicing junctions. 763 known splicing junctions. 1343 novel splicing junctions.
sampling 25% (5497) splicing reads. 2378 splicing junctions. 821 known splicing junctions. 1557 novel splicing junctions.
sampling 30% (6597) splicing reads. 2627 splicing junctions. 858 known splicing junctions. 1769 novel splicing junctions.
sampling 35% (7696) splicing reads. 2829 splicing junctions. 895 known splicing junctions. 1934 novel splicing junctions.
sampling 40% (8796) splicing reads. 3034 splicing junctions. 929 known splicing junctions. 2105 novel splicing junctions.
sampling 45% (9895) splicing reads. 3197 splicing junctions. 955 known splicing junctions. 2242 novel splicing junctions.
sampling 50% (10995) splicing reads. 3352 splicing junctions. 978 known splicing junctions. 2374 novel splicing junctions.
sampling 55% (12094) splicing reads. 3490 splicing junctions. 993 known splicing junctions. 2497 novel splicing junctions.
sampling 60% (13194) splicing reads. 3610 splicing junctions. 1007 known splicing junctions. 2603 novel splicing junctions.
sampling 65% (14293) splicing reads. 3716 splicing junctions. 1019 known splicing junctions. 2697 novel splicing junctions.
sampling 70% (15392) splicing reads. 3811 splicing junctions. 1032 known splicing junctions. 2779 novel splicing junctions.
sampling 75% (16492) splicing reads. 3899 splicing junctions. 1042 known splicing junctions. 2857 novel splicing junctions.
sampling 80% (17592) splicing reads. 3964 splicing junctions. 1052 known splicing junctions. 2912 novel splicing junctions.
sampling 85% (18691) splicing reads. 4024 splicing junctions. 1059 known splicing junctions. 2965 novel splicing junctions.
sampling 90% (19791) splicing reads. 4060 splicing junctions. 1061 known splicing junctions. 2999 novel splicing junctions.
sampling 95% (20890) splicing reads. 4119 splicing junctions. 1066 known splicing junctions. 3053 novel splicing junctions.
sampling 100% (21990) splicing reads. 4153 splicing junctions. 1070 known splicing junctions. 3083 novel splicing junctions.