[W::hts_idx_load3] The index file is older than the data file: 659_w_T1_TRNA_1_B2372Y3LT4_1.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% (4759209) splicing reads. 172107 splicing junctions. 143337 known splicing junctions. 28770 novel splicing junctions.
sampling 10% (9518419) splicing reads. 202659 splicing junctions. 158546 known splicing junctions. 44113 novel splicing junctions.
sampling 15% (14277628) splicing reads. 220878 splicing junctions. 165832 known splicing junctions. 55046 novel splicing junctions.
sampling 20% (19036838) splicing reads. 233754 splicing junctions. 170486 known splicing junctions. 63268 novel splicing junctions.
sampling 25% (23796048) splicing reads. 243390 splicing junctions. 173598 known splicing junctions. 69792 novel splicing junctions.
sampling 30% (28555257) splicing reads. 251178 splicing junctions. 175966 known splicing junctions. 75212 novel splicing junctions.
sampling 35% (33314467) splicing reads. 257193 splicing junctions. 177697 known splicing junctions. 79496 novel splicing junctions.
sampling 40% (38073677) splicing reads. 262247 splicing junctions. 179058 known splicing junctions. 83189 novel splicing junctions.
sampling 45% (42832886) splicing reads. 266477 splicing junctions. 180159 known splicing junctions. 86318 novel splicing junctions.
sampling 50% (47592096) splicing reads. 270108 splicing junctions. 181072 known splicing junctions. 89036 novel splicing junctions.
sampling 55% (52351306) splicing reads. 273287 splicing junctions. 181843 known splicing junctions. 91444 novel splicing junctions.
sampling 60% (57110515) splicing reads. 275974 splicing junctions. 182474 known splicing junctions. 93500 novel splicing junctions.
sampling 65% (61869725) splicing reads. 278242 splicing junctions. 182965 known splicing junctions. 95277 novel splicing junctions.
sampling 70% (66628935) splicing reads. 280310 splicing junctions. 183412 known splicing junctions. 96898 novel splicing junctions.
sampling 75% (71388144) splicing reads. 281963 splicing junctions. 183791 known splicing junctions. 98172 novel splicing junctions.
sampling 80% (76147354) splicing reads. 283389 splicing junctions. 184122 known splicing junctions. 99267 novel splicing junctions.
sampling 85% (80906564) splicing reads. 284611 splicing junctions. 184363 known splicing junctions. 100248 novel splicing junctions.
sampling 90% (85665773) splicing reads. 285676 splicing junctions. 184580 known splicing junctions. 101096 novel splicing junctions.
sampling 95% (90424983) splicing reads. 286484 splicing junctions. 184765 known splicing junctions. 101719 novel splicing junctions.
sampling 100% (95184193) splicing reads. 287117 splicing junctions. 184895 known splicing junctions. 102222 novel splicing junctions.