homebrew/science bowtie not working correctly

[traeki]

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

[dpryan]

You'll probably be best off taking this up with whomever is in charge of that homebrew formula.

[traeki]

Well, I'm assuming that if this were caused by the brew script per se, the most recent update thereof would be more recent than July (I can't be the only one actively using homebrew with bowtie).

What I'm trying to figure out is what could possibly cause bowtie to behave this way. One test I haven't done, but might try tomorrow, is to download the source and build it manually. Perhaps there's somehow something wrong with my build environment?

In the meantime I'm hoping somebody else has actually experienced this and will recognize the problem of which this is a symptom.

Thanks,

-John

[dpryan]

Well, I'm assuming that if this were caused by the brew script per se, the most recent update thereof would be more recent than July (I can't be the only one actively using homebrew with bowtie).

Don't be so sure about that.

BTW, what exactly do you mean by "alien binary output"? Just binary gibberish?

[traeki]

The original post contains a tar file with the two files generated by the two binaries. "bad.bowtie" is the gibberish form.

EDIT: the short answer is "yes", though it looks like structured gibberish, with a semi-repetitive pattern, as though bowtie is outputting compressed records or internal state or something instead of printing human-readable lines.

[dpryan]

Ah, that's certainly gibberish.

[traeki]

Yeah, and what's weird is that if I generate SAM output, the headers are non-gibberish. So it's capable of printing normal text, it's just ... choosing not to when it actually matters. ::sigh::

[traeki]

Okay, my computer must be the problem -- I've tried re-building the binaries from scratch, outside of homebrew, and I get the same garbage output symptom. So now I guess the question is, what would cause my build to generate a bowtie binary that can't produce sensible output?

Thanks,

-John

[traeki]

For anybody coming across this later:

There's apparently a problem after the Mavericks release that under some circumstances causes bad builds because of the particulars of glibc++ and related infrastructure.

The bowtie folks have a fix that seems to resolve this at least in my case (phew!) and are planning a bowtie release in the relatively near future (days, not months).

So, if you're having this same problem, take heart. And if you're urgently desperate, pull from the git master of bowtie directly.