I'm running a macbook pro with OS X Mavericks (10.9). I have bowtie installed under homebrew. I also (while exploring this problem) installed the most recent OS X binaries for bowtie directly.
When I run the downloaded binaries, everything seems normal. But when I run the exact same command with the homebrew installation (homebrew of course is compiling locally from source), I get alien binary output from bowtie, no matter what output format I request. Notably, for sam output (not attached) the headers look normal, bowtie just vomits garbage for the reads themselves.
I've attached examples of the good and bad output, generated using the command from the tutorial...
bowtie indexes/e_coli reads/e_coli_1000.fq
...but using either ./bowtie (the pre-built binary) to generate good output, or bowtie (my homebrew installation) to generate the bad output.
I've tried uninstalling homebrew completely and rebuilding from the ground up, to no avail.
What could be going wrong?! What might cause this problem? Help!!
Thanks,
-John
When I run the downloaded binaries, everything seems normal. But when I run the exact same command with the homebrew installation (homebrew of course is compiling locally from source), I get alien binary output from bowtie, no matter what output format I request. Notably, for sam output (not attached) the headers look normal, bowtie just vomits garbage for the reads themselves.
I've attached examples of the good and bad output, generated using the command from the tutorial...
bowtie indexes/e_coli reads/e_coli_1000.fq
...but using either ./bowtie (the pre-built binary) to generate good output, or bowtie (my homebrew installation) to generate the bad output.
I've tried uninstalling homebrew completely and rebuilding from the ground up, to no avail.
What could be going wrong?! What might cause this problem? Help!!
Thanks,
-John
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