[W::hts_idx_load3] The index file is older than the data file: dna_s774.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% (20418) splicing reads. 5311 splicing junctions. 1357 known splicing junctions. 3954 novel splicing junctions.
sampling 10% (40837) splicing reads. 8020 splicing junctions. 1601 known splicing junctions. 6419 novel splicing junctions.
sampling 15% (61255) splicing reads. 10175 splicing junctions. 1734 known splicing junctions. 8441 novel splicing junctions.
sampling 20% (81674) splicing reads. 11988 splicing junctions. 1821 known splicing junctions. 10167 novel splicing junctions.
sampling 25% (102093) splicing reads. 13592 splicing junctions. 1871 known splicing junctions. 11721 novel splicing junctions.
sampling 30% (122511) splicing reads. 14995 splicing junctions. 1925 known splicing junctions. 13070 novel splicing junctions.
sampling 35% (142930) splicing reads. 16238 splicing junctions. 1961 known splicing junctions. 14277 novel splicing junctions.
sampling 40% (163349) splicing reads. 17353 splicing junctions. 1998 known splicing junctions. 15355 novel splicing junctions.
sampling 45% (183767) splicing reads. 18417 splicing junctions. 2023 known splicing junctions. 16394 novel splicing junctions.
sampling 50% (204186) splicing reads. 19407 splicing junctions. 2046 known splicing junctions. 17361 novel splicing junctions.
sampling 55% (224605) splicing reads. 20317 splicing junctions. 2070 known splicing junctions. 18247 novel splicing junctions.
sampling 60% (245023) splicing reads. 21136 splicing junctions. 2089 known splicing junctions. 19047 novel splicing junctions.
sampling 65% (265442) splicing reads. 21920 splicing junctions. 2106 known splicing junctions. 19814 novel splicing junctions.
sampling 70% (285861) splicing reads. 22649 splicing junctions. 2122 known splicing junctions. 20527 novel splicing junctions.
sampling 75% (306279) splicing reads. 23274 splicing junctions. 2137 known splicing junctions. 21137 novel splicing junctions.
sampling 80% (326698) splicing reads. 23876 splicing junctions. 2143 known splicing junctions. 21733 novel splicing junctions.
sampling 85% (347117) splicing reads. 24469 splicing junctions. 2152 known splicing junctions. 22317 novel splicing junctions.
sampling 90% (367535) splicing reads. 24980 splicing junctions. 2158 known splicing junctions. 22822 novel splicing junctions.
sampling 95% (387954) splicing reads. 25401 splicing junctions. 2162 known splicing junctions. 23239 novel splicing junctions.
sampling 100% (408373) splicing reads. 25806 splicing junctions. 2165 known splicing junctions. 23641 novel splicing junctions.