[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. 93956 splicing junctions. 89547 known splicing junctions. 4409 novel splicing junctions.
sampling 10% (1121740) splicing reads. 112651 splicing junctions. 104738 known splicing junctions. 7913 novel splicing junctions.
sampling 15% (1682611) splicing reads. 123589 splicing junctions. 112514 known splicing junctions. 11075 novel splicing junctions.
sampling 20% (2243481) splicing reads. 131387 splicing junctions. 117555 known splicing junctions. 13832 novel splicing junctions.
sampling 25% (2804352) splicing reads. 137528 splicing junctions. 121175 known splicing junctions. 16353 novel splicing junctions.
sampling 30% (3365222) splicing reads. 142671 splicing junctions. 124024 known splicing junctions. 18647 novel splicing junctions.
sampling 35% (3926092) splicing reads. 146981 splicing junctions. 126279 known splicing junctions. 20702 novel splicing junctions.
sampling 40% (4486963) splicing reads. 150806 splicing junctions. 128209 known splicing junctions. 22597 novel splicing junctions.
sampling 45% (5047833) splicing reads. 154150 splicing junctions. 129852 known splicing junctions. 24298 novel splicing junctions.
sampling 50% (5608704) splicing reads. 157241 splicing junctions. 131277 known splicing junctions. 25964 novel splicing junctions.
sampling 55% (6169574) splicing reads. 160044 splicing junctions. 132491 known splicing junctions. 27553 novel splicing junctions.
sampling 60% (6730444) splicing reads. 162505 splicing junctions. 133591 known splicing junctions. 28914 novel splicing junctions.
sampling 65% (7291315) splicing reads. 164806 splicing junctions. 134578 known splicing junctions. 30228 novel splicing junctions.
sampling 70% (7852185) splicing reads. 166874 splicing junctions. 135471 known splicing junctions. 31403 novel splicing junctions.
sampling 75% (8413056) splicing reads. 168780 splicing junctions. 136223 known splicing junctions. 32557 novel splicing junctions.
sampling 80% (8973926) splicing reads. 170470 splicing junctions. 136875 known splicing junctions. 33595 novel splicing junctions.
sampling 85% (9534796) splicing reads. 172028 splicing junctions. 137532 known splicing junctions. 34496 novel splicing junctions.
sampling 90% (10095667) splicing reads. 173390 splicing junctions. 138039 known splicing junctions. 35351 novel splicing junctions.
sampling 95% (10656537) splicing reads. 174667 splicing junctions. 138538 known splicing junctions. 36129 novel splicing junctions.
sampling 100% (11217408) splicing reads. 175815 splicing junctions. 139001 known splicing junctions. 36814 novel splicing junctions.