[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. 94057 splicing junctions. 89624 known splicing junctions. 4433 novel splicing junctions.
sampling 10% (1121824) splicing reads. 112686 splicing junctions. 104740 known splicing junctions. 7946 novel splicing junctions.
sampling 15% (1682736) splicing reads. 123501 splicing junctions. 112399 known splicing junctions. 11102 novel splicing junctions.
sampling 20% (2243649) splicing reads. 131196 splicing junctions. 117314 known splicing junctions. 13882 novel splicing junctions.
sampling 25% (2804561) splicing reads. 137329 splicing junctions. 120969 known splicing junctions. 16360 novel splicing junctions.
sampling 30% (3365473) splicing reads. 142527 splicing junctions. 123810 known splicing junctions. 18717 novel splicing junctions.
sampling 35% (3926385) splicing reads. 147007 splicing junctions. 126167 known splicing junctions. 20840 novel splicing junctions.
sampling 40% (4487298) splicing reads. 151021 splicing junctions. 128148 known splicing junctions. 22873 novel splicing junctions.
sampling 45% (5048210) splicing reads. 154416 splicing junctions. 129804 known splicing junctions. 24612 novel splicing junctions.
sampling 50% (5609122) splicing reads. 157589 splicing junctions. 131294 known splicing junctions. 26295 novel splicing junctions.
sampling 55% (6170034) splicing reads. 160429 splicing junctions. 132581 known splicing junctions. 27848 novel splicing junctions.
sampling 60% (6730947) splicing reads. 162814 splicing junctions. 133611 known splicing junctions. 29203 novel splicing junctions.
sampling 65% (7291859) splicing reads. 165079 splicing junctions. 134552 known splicing junctions. 30527 novel splicing junctions.
sampling 70% (7852771) splicing reads. 167125 splicing junctions. 135405 known splicing junctions. 31720 novel splicing junctions.
sampling 75% (8413683) splicing reads. 169023 splicing junctions. 136172 known splicing junctions. 32851 novel splicing junctions.
sampling 80% (8974596) splicing reads. 170761 splicing junctions. 136863 known splicing junctions. 33898 novel splicing junctions.
sampling 85% (9535508) splicing reads. 172297 splicing junctions. 137544 known splicing junctions. 34753 novel splicing junctions.
sampling 90% (10096420) splicing reads. 173728 splicing junctions. 138086 known splicing junctions. 35642 novel splicing junctions.
sampling 95% (10657332) splicing reads. 175020 splicing junctions. 138574 known splicing junctions. 36446 novel splicing junctions.
sampling 100% (11218245) splicing reads. 176197 splicing junctions. 139062 known splicing junctions. 37135 novel splicing junctions.