I'm seeing the error below when I try to run Tophat for Illumina. Has anyone seen this before? Could I have installed bowtie incorrectly or am I simply running with the wrong data/parameters? Thanks, Greg (I'm also really confused why the error is mentioned /tmp/* paths. I never assigned anything to /tmp in the universe_wsgi.ini. Where is it getting that from?) Error in tophat: [2012-12-13 13:55:01] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-12-13 13:55:01] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-13 13:55:01] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-13 13:55:01] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)