[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. 96009 splicing junctions. 91335 known splicing junctions. 4674 novel splicing junctions.
sampling 10% (1173971) splicing reads. 114853 splicing junctions. 106352 known splicing junctions. 8501 novel splicing junctions.
sampling 15% (1760957) splicing reads. 125471 splicing junctions. 113768 known splicing junctions. 11703 novel splicing junctions.
sampling 20% (2347942) splicing reads. 133431 splicing junctions. 118803 known splicing junctions. 14628 novel splicing junctions.
sampling 25% (2934928) splicing reads. 139666 splicing junctions. 122296 known splicing junctions. 17370 novel splicing junctions.
sampling 30% (3521914) splicing reads. 144850 splicing junctions. 125138 known splicing junctions. 19712 novel splicing junctions.
sampling 35% (4108899) splicing reads. 149317 splicing junctions. 127421 known splicing junctions. 21896 novel splicing junctions.
sampling 40% (4695885) splicing reads. 153317 splicing junctions. 129367 known splicing junctions. 23950 novel splicing junctions.
sampling 45% (5282871) splicing reads. 156884 splicing junctions. 131015 known splicing junctions. 25869 novel splicing junctions.
sampling 50% (5869857) splicing reads. 159964 splicing junctions. 132414 known splicing junctions. 27550 novel splicing junctions.
sampling 55% (6456842) splicing reads. 162856 splicing junctions. 133719 known splicing junctions. 29137 novel splicing junctions.
sampling 60% (7043828) splicing reads. 165426 splicing junctions. 134854 known splicing junctions. 30572 novel splicing junctions.
sampling 65% (7630814) splicing reads. 167828 splicing junctions. 135896 known splicing junctions. 31932 novel splicing junctions.
sampling 70% (8217799) splicing reads. 170039 splicing junctions. 136799 known splicing junctions. 33240 novel splicing junctions.
sampling 75% (8804785) splicing reads. 172056 splicing junctions. 137592 known splicing junctions. 34464 novel splicing junctions.
sampling 80% (9391771) splicing reads. 173862 splicing junctions. 138320 known splicing junctions. 35542 novel splicing junctions.
sampling 85% (9978756) splicing reads. 175505 splicing junctions. 138980 known splicing junctions. 36525 novel splicing junctions.
sampling 90% (10565742) splicing reads. 177063 splicing junctions. 139595 known splicing junctions. 37468 novel splicing junctions.
sampling 95% (11152728) splicing reads. 178475 splicing junctions. 140137 known splicing junctions. 38338 novel splicing junctions.
sampling 100% (11739714) splicing reads. 179686 splicing junctions. 140590 known splicing junctions. 39096 novel splicing junctions.