tophat_reports v2.0.8 (3864) --------------------------------------- [samopen] SAM header is present: 1202 sequences. 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scaffold_1157...done Loading scaffold_1158...done Loading scaffold_1159...done Loading scaffold_1160...done Loading scaffold_1161...done Loading scaffold_1162...done Loading scaffold_1163...done Loading scaffold_1164...done Loading scaffold_1165...done Loading scaffold_1166...done Loading scaffold_1167...done Loading scaffold_1168...done Loading scaffold_1169...done Loading scaffold_1170...done Loading scaffold_1171...done Loading scaffold_1172...done Loading scaffold_1173...done Loading scaffold_1174...done Loading scaffold_1175...done Loading scaffold_1176...done Loading scaffold_1177...done Loading scaffold_1178...done Loading scaffold_1179...done Loading scaffold_1180...done Loading scaffold_1181...done Loading scaffold_1182...done Loading scaffold_1183...done Loading scaffold_1184...done Loading scaffold_1185...done Loading scaffold_1186...done Loading scaffold_1187...done Loading scaffold_1188...done Loading scaffold_1189...done Loading scaffold_1190...done Loading scaffold_1191...done Loading scaffold_1192...done Loading scaffold_1193...done Loading scaffold_1194...done Loading scaffold_1195...done Loading scaffold_1196...done Loading scaffold_1197...done Loading scaffold_1198...done Loading scaffold_1199...done Loading scaffold_1200...done Loading scaffold_1201...done Loading scaffold_1202...done Loading ...done Loaded 45494 GFF junctions from Paramecium-caudatum-no-Hol_S15-2x100-TopHat-2.0.8-minIntron10/tmp/caudatum_43c3d_annotation_v1.juncs. Loaded 61260 junctions Reporting final accepted alignments...done. Printing junction BED track...done Printing insertions...done Printing deletions...done Found 46282 junctions from happy spliced reads