Hi, I actually fixed it. I changed the wrapper in the line 105 from: cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file, index_path ) to cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file, index_path ) Luciano On Tue, Jun 19, 2012 at 3:03 PM, Luciano Cosme <cosme.simple@gmail.com>wrote:

Hi, I installed bowtie2 and when running tophat I get the following error:

Error in tophat:

[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3) ----------------------------------------------- [2012-06-19 14:02:39] Checking for Bowtie Bowtie version: 2.0.0.6 [2012-06-19 14:02:39] Checking for Samtools Samtools version: 0.1.18.0 [2012-06-19 14:02:39] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)

I was wondering if I can create the index files using bowtie2 via command line and then change the universe_wsgi.ini to: # Temporary files are stored in this directory. new_file_path = database/tmp

and put the index files there. Anyway, why is it not creating the indexes? I created links to all bowtie2 executable files. If I remove bowtie 0.12.8, then I get a error from tophat (bowtie not installed). Is it creating the index with bowtie 0.12.8? Thank you.

Luciano

-- *Luciano Cosme* --------------------------------------------- PhD Candidate Texas A&M Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 cosme@tamu.edu ---------------------------------------------