tophat_reports v2.0.8 (3864) --------------------------------------- [samopen] SAM header is present: 677 sequences. 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scaffold_675...done Loading scaffold_676...done Loading scaffold_677...done Loading ...done Loaded 99002 GFF junctions from Paramecium_primaurelia-GSF869-Doak-Ugne-227_S13-2x100-TopHat-2.0.8-minIntron10//tmp/primaurelia_Ir4-2_annotation_v1.juncs. Loaded 126954 junctions Reporting final accepted alignments...done. Printing junction BED track...done Printing insertions...done Printing deletions...done Found 93850 junctions from happy spliced reads