Bowtie Error On Os X: "Illegal Instruction"

Question

[datanerd]

Hi all,

I have installed bowtie for macox and moved it to the bin folder and ran bowtie,

bowtie -S -p 2 indexfile -1 /input.fastq -2 /output.sam

but i get an error as "illegal instruction"

Could someone suggest what might the problem be?

thanks!!!

[Ashutosh Pandey]

First of all I would recommend you to use bowtie2. I would only prefer using bowtie if i have to align colorspace reads which bowtie2 doesnt support. Now coming to your question, there could be one or many problem with your command line. /input.fastq means that your fastq file is located in your root directory which I think is completely wrong. Look into some unix tutorial and learn how to give the correct path. Also, -2 is only required when you have paired end data. I suppose you only have single end reads , so remove -2. Also your are trying to generate your output file in root directory. Look at the manual carefully and try again: http://bowtie-bio.sourceforge.net/manual.shtml

[datanerd]

Thanks for the reply, But I am kinda familiar with the unix command, and my path was NOT in the root directory but i had specified the path. Just for the sake of keeping it simple i wrote that (yea, i should have mentioned/path to/, my bad) and that 2 isnt for paired, i guess -p specifies cores.

[datanerd]

ok.. got it, the other 2, yes, iam not using that that anymore.

[Ashutosh Pandey]

Great. Let me know if you have other problems.

[Sukhi Singh]

Can you also add this an answer!!

[Ashutosh Pandey]

Sure. I shud have done that.

Answer 1

[Roman Valls Guimerà]

Illegal instructions normally happen when you try to run compiled code from one CPU (sub)architecture to another.

Even the so-called sub-architectures can produce these problems (i.e: code compiled with an AMD Bulldozer with AVX instructions/optimizations will not run on an Intel Core 7).

How did you compile Bowtie? If you compiled it in one machine and moved the resulting binary to another (x86_32 vs x86_64) that's a typical issue. Even in academic clusters where they share the binary base via non-standard, deprecated and not community-supported packaging management systems, that can happen easily.

Since you are using a Mac, installing Homebrew and running brew install bowtie should be enough to get you going.

Well, apparently brew tap homebrew/science and brew install bowtie2 with newest homebrew.

Hope that helps!

[datanerd]

Thanks! But bowtie was precompiled when i installed it, so i didnot do any compiling. I can use bowtie2 but can't yet understand what is wrong with bowtie. I was more keen in using bowtie because it lets me get the uniquely mapping reads.

[Roman Valls Guimerà]

It was precompiled from where, who (pre)compiled it? Where did you get it from?

Did you try to install Homebrew as suggested? As a mac user, it'll really simplify your package management, no need to copy binaries anymore.

Answer 2

[Ashutosh Pandey]

First of all I would recommend you to use bowtie2. I would only prefer using bowtie if i have to align colorspace reads which bowtie2 doesnt support. Now coming to your question, there could be one or many problem with your command line. /input.fastq means that your fastq file is located in your root directory which I think is completely wrong. Look into some unix tutorial and learn how to give the correct path. Also, -2 is only required when you have paired end data. I suppose you only have single end reads , so remove -2. Also your are trying to generate your output file in root directory. Look at the manual carefully and try again: http://bowtie-bio.sourceforge.net/manual.shtml