[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_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% (856730) splicing reads. 81506 splicing junctions. 78349 known splicing junctions. 3157 novel splicing junctions.
sampling 10% (1713460) splicing reads. 89951 splicing junctions. 85917 known splicing junctions. 4034 novel splicing junctions.
sampling 15% (2570190) splicing reads. 93257 splicing junctions. 88777 known splicing junctions. 4480 novel splicing junctions.
sampling 20% (3426920) splicing reads. 95072 splicing junctions. 90258 known splicing junctions. 4814 novel splicing junctions.
sampling 25% (4283650) splicing reads. 96285 splicing junctions. 91197 known splicing junctions. 5088 novel splicing junctions.
sampling 30% (5140380) splicing reads. 97198 splicing junctions. 91881 known splicing junctions. 5317 novel splicing junctions.
sampling 35% (5997110) splicing reads. 97942 splicing junctions. 92419 known splicing junctions. 5523 novel splicing junctions.
sampling 40% (6853840) splicing reads. 98460 splicing junctions. 92782 known splicing junctions. 5678 novel splicing junctions.
sampling 45% (7710570) splicing reads. 98941 splicing junctions. 93106 known splicing junctions. 5835 novel splicing junctions.
sampling 50% (8567301) splicing reads. 99346 splicing junctions. 93382 known splicing junctions. 5964 novel splicing junctions.
sampling 55% (9424031) splicing reads. 99668 splicing junctions. 93599 known splicing junctions. 6069 novel splicing junctions.
sampling 60% (10280761) splicing reads. 99927 splicing junctions. 93759 known splicing junctions. 6168 novel splicing junctions.
sampling 65% (11137491) splicing reads. 100147 splicing junctions. 93891 known splicing junctions. 6256 novel splicing junctions.
sampling 70% (11994221) splicing reads. 100344 splicing junctions. 94016 known splicing junctions. 6328 novel splicing junctions.
sampling 75% (12850951) splicing reads. 100496 splicing junctions. 94108 known splicing junctions. 6388 novel splicing junctions.
sampling 80% (13707681) splicing reads. 100621 splicing junctions. 94185 known splicing junctions. 6436 novel splicing junctions.
sampling 85% (14564411) splicing reads. 100723 splicing junctions. 94245 known splicing junctions. 6478 novel splicing junctions.
sampling 90% (15421141) splicing reads. 100810 splicing junctions. 94288 known splicing junctions. 6522 novel splicing junctions.
sampling 95% (16277871) splicing reads. 100866 splicing junctions. 94322 known splicing junctions. 6544 novel splicing junctions.
sampling 100% (17134602) splicing reads. 100883 splicing junctions. 94328 known splicing junctions. 6555 novel splicing junctions.