[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.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% (143710) splicing reads. 32592 splicing junctions. 31482 known splicing junctions. 1110 novel splicing junctions.
sampling 10% (287421) splicing reads. 38679 splicing junctions. 37265 known splicing junctions. 1414 novel splicing junctions.
sampling 15% (431132) splicing reads. 41304 splicing junctions. 39683 known splicing junctions. 1621 novel splicing junctions.
sampling 20% (574843) splicing reads. 42889 splicing junctions. 41095 known splicing junctions. 1794 novel splicing junctions.
sampling 25% (718554) splicing reads. 43945 splicing junctions. 42036 known splicing junctions. 1909 novel splicing junctions.
sampling 30% (862265) splicing reads. 44710 splicing junctions. 42692 known splicing junctions. 2018 novel splicing junctions.
sampling 35% (1005975) splicing reads. 45334 splicing junctions. 43232 known splicing junctions. 2102 novel splicing junctions.
sampling 40% (1149686) splicing reads. 45772 splicing junctions. 43593 known splicing junctions. 2179 novel splicing junctions.
sampling 45% (1293397) splicing reads. 46141 splicing junctions. 43893 known splicing junctions. 2248 novel splicing junctions.
sampling 50% (1437108) splicing reads. 46435 splicing junctions. 44133 known splicing junctions. 2302 novel splicing junctions.
sampling 55% (1580819) splicing reads. 46685 splicing junctions. 44326 known splicing junctions. 2359 novel splicing junctions.
sampling 60% (1724530) splicing reads. 46898 splicing junctions. 44494 known splicing junctions. 2404 novel splicing junctions.
sampling 65% (1868241) splicing reads. 47085 splicing junctions. 44639 known splicing junctions. 2446 novel splicing junctions.
sampling 70% (2011951) splicing reads. 47222 splicing junctions. 44745 known splicing junctions. 2477 novel splicing junctions.
sampling 75% (2155662) splicing reads. 47338 splicing junctions. 44834 known splicing junctions. 2504 novel splicing junctions.
sampling 80% (2299373) splicing reads. 47421 splicing junctions. 44901 known splicing junctions. 2520 novel splicing junctions.
sampling 85% (2443084) splicing reads. 47484 splicing junctions. 44945 known splicing junctions. 2539 novel splicing junctions.
sampling 90% (2586795) splicing reads. 47543 splicing junctions. 44989 known splicing junctions. 2554 novel splicing junctions.
sampling 95% (2730506) splicing reads. 47573 splicing junctions. 45013 known splicing junctions. 2560 novel splicing junctions.
sampling 100% (2874217) splicing reads. 47585 splicing junctions. 45024 known splicing junctions. 2561 novel splicing junctions.