tophat_reports v2.0.8 (3864) --------------------------------------- [samopen] SAM header is present: 1878 sequences. 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scaffold_1768...done Loading scaffold_1769...done Loading scaffold_1770...done Loading scaffold_1771...done Loading scaffold_1772...done Loading scaffold_1773...done Loading scaffold_1774...done Loading scaffold_1775...done Loading scaffold_1776...done Loading scaffold_1777...done Loading scaffold_1778...done Loading scaffold_1779...done Loading scaffold_1780...done Loading scaffold_1781...done Loading scaffold_1782...done Loading scaffold_1783...done Loading scaffold_1784...done Loading scaffold_1785...done Loading scaffold_1786...done Loading scaffold_1787...done Loading scaffold_1788...done Loading scaffold_1789...done Loading scaffold_1790...done Loading scaffold_1791...done Loading scaffold_1792...done Loading scaffold_1793...done Loading scaffold_1794...done Loading scaffold_1795...done Loading scaffold_1796...done Loading scaffold_1797...done Loading scaffold_1798...done Loading scaffold_1799...done Loading scaffold_1800...done Loading scaffold_1801...done Loading scaffold_1802...done Loading scaffold_1803...done Loading scaffold_1804...done Loading scaffold_1805...done Loading scaffold_1806...done Loading scaffold_1807...done Loading scaffold_1808...done Loading scaffold_1809...done Loading scaffold_1810...done Loading scaffold_1811...done Loading scaffold_1812...done Loading scaffold_1813...done Loading scaffold_1814...done Loading scaffold_1815...done Loading scaffold_1816...done Loading scaffold_1817...done Loading scaffold_1818...done Loading scaffold_1819...done Loading scaffold_1820...done Loading scaffold_1821...done Loading scaffold_1822...done Loading scaffold_1823...done Loading scaffold_1824...done Loading scaffold_1825...done Loading scaffold_1826...done Loading scaffold_1827...done Loading scaffold_1828...done Loading scaffold_1829...done Loading scaffold_1830...done Loading scaffold_1831...done Loading scaffold_1832...done Loading scaffold_1833...done Loading scaffold_1834...done Loading scaffold_1835...done Loading scaffold_1836...done Loading scaffold_1837...done Loading scaffold_1838...done Loading scaffold_1839...done Loading scaffold_1840...done Loading scaffold_1841...done Loading scaffold_1842...done Loading scaffold_1843...done Loading scaffold_1844...done Loading scaffold_1845...done Loading scaffold_1846...done Loading scaffold_1847...done Loading scaffold_1848...done Loading scaffold_1849...done Loading scaffold_1850...done Loading scaffold_1851...done Loading scaffold_1852...done Loading scaffold_1853...done Loading scaffold_1854...done Loading scaffold_1855...done Loading scaffold_1856...done Loading scaffold_1857...done Loading scaffold_1858...done Loading scaffold_1859...done Loading scaffold_1860...done Loading scaffold_1861...done Loading scaffold_1862...done Loading scaffold_1863...done Loading scaffold_1864...done Loading scaffold_1865...done Loading scaffold_1866...done Loading scaffold_1867...done Loading scaffold_1868...done Loading scaffold_1869...done Loading scaffold_1870...done Loading scaffold_1871...done Loading scaffold_1872...done Loading scaffold_1873...done Loading scaffold_1874...done Loading scaffold_1875...done Loading scaffold_1876...done Loading scaffold_1877...done Loading ...done Loaded 84918 GFF junctions from Paramecium_novaurelia-TE-GSF1240-N1_S5-2x80-TopHat-2.0.8-minIntron10-genome+mito/tmp/pnovaurelia_TE_annotation_v1.juncs. Loaded 125309 junctions Reporting final accepted alignments...done. Printing junction BED track...done Printing insertions...done Printing deletions...done Found 109102 junctions from happy spliced reads