Hi Everyone,
After my previous installed tophat/bowtie versions worked without a problem, I wanted to update to the newest versions and also installed tophat2 and bowtie2. Both programs have links to them from the /bin directory which is in the path.
When trying to run the running example, tophat2 claims I do not have the correct version of bowtie installed. I'm a UNIX newbie and would appreciate any help and ideas!
Thanks!
After my previous installed tophat/bowtie versions worked without a problem, I wanted to update to the newest versions and also installed tophat2 and bowtie2. Both programs have links to them from the /bin directory which is in the path.
When trying to run the running example, tophat2 claims I do not have the correct version of bowtie installed. I'm a UNIX newbie and would appreciate any help and ideas!
Thanks!
Code:
[galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ bowtie --version bowtie version 0.12.5 64-bit Built on sycamore.umiacs.umd.edu Sat Apr 24 15:56:29 EDT 2010 Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46) Options: -O3 -m64 -Wl,--hash-style=both Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ bowtie2 --version /bin/bowtie2-align version 2.1.0 64-bit Built on igm3 Thu Feb 21 09:33:38 EST 2013 Compiler: gcc version 4.5.4 (GCC) Options: -O3 -m64 -msse2 -funroll-loops -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ tophat2 --version TopHat v2.0.7 [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ [galaxy01@gene3 test_data]$ tophat2 test_ref reads_1.fq reads_2.fq [2013-02-26 09:35:20] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-02-26 09:35:20] Checking for Bowtie Error: TopHat requires Bowtie 2.0.5 or later [galaxy01@gene3 test_data]$
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