[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.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% (586985) splicing reads. 95902 splicing junctions. 91226 known splicing junctions. 4676 novel splicing junctions.
sampling 10% (1173971) splicing reads. 114777 splicing junctions. 106268 known splicing junctions. 8509 novel splicing junctions.
sampling 15% (1760957) splicing reads. 125682 splicing junctions. 113875 known splicing junctions. 11807 novel splicing junctions.
sampling 20% (2347942) splicing reads. 133549 splicing junctions. 118773 known splicing junctions. 14776 novel splicing junctions.
sampling 25% (2934928) splicing reads. 139932 splicing junctions. 122433 known splicing junctions. 17499 novel splicing junctions.
sampling 30% (3521914) splicing reads. 145149 splicing junctions. 125257 known splicing junctions. 19892 novel splicing junctions.
sampling 35% (4108899) splicing reads. 149797 splicing junctions. 127616 known splicing junctions. 22181 novel splicing junctions.
sampling 40% (4695885) splicing reads. 153701 splicing junctions. 129546 known splicing junctions. 24155 novel splicing junctions.
sampling 45% (5282871) splicing reads. 157315 splicing junctions. 131277 known splicing junctions. 26038 novel splicing junctions.
sampling 50% (5869857) splicing reads. 160428 splicing junctions. 132665 known splicing junctions. 27763 novel splicing junctions.
sampling 55% (6456842) splicing reads. 163267 splicing junctions. 133913 known splicing junctions. 29354 novel splicing junctions.
sampling 60% (7043828) splicing reads. 165813 splicing junctions. 135015 known splicing junctions. 30798 novel splicing junctions.
sampling 65% (7630814) splicing reads. 168152 splicing junctions. 135941 known splicing junctions. 32211 novel splicing junctions.
sampling 70% (8217799) splicing reads. 170303 splicing junctions. 136801 known splicing junctions. 33502 novel splicing junctions.
sampling 75% (8804785) splicing reads. 172291 splicing junctions. 137624 known splicing junctions. 34667 novel splicing junctions.
sampling 80% (9391771) splicing reads. 174125 splicing junctions. 138381 known splicing junctions. 35744 novel splicing junctions.
sampling 85% (9978756) splicing reads. 175726 splicing junctions. 139049 known splicing junctions. 36677 novel splicing junctions.
sampling 90% (10565742) splicing reads. 177212 splicing junctions. 139648 known splicing junctions. 37564 novel splicing junctions.
sampling 95% (11152728) splicing reads. 178543 splicing junctions. 140141 known splicing junctions. 38402 novel splicing junctions.
sampling 100% (11739714) splicing reads. 179686 splicing junctions. 140590 known splicing junctions. 39096 novel splicing junctions.