Tophat2, Tophat, Bowtie2 returns the empty file. The output is in the format:<div><br></div><div><i>Galaxy5-[Bowtie2_on_data_4__mapped_reads]</i></div><div><br></div><div>Whenever I open it by double clicking I get the empty file which 0 bytes file size. I am using hg19 index. What might be the problem? </div>