Update newest BWA version - Error

[Superbug]

Hey

I tried to update my bwa version today to the latest one (http://sourceforge.net/projects/bio-bwa/files/)!

I performed these commands:

tar jxf bwa-0.7.9.tar.bz2
cd bwa-0.7.9
make

And then I get an error message!

I really need the latest version to map my reads as some of them don't work with the version I have

[mastal]

What was the error message you got, and what OS are you using?

[Superbug]

I am running Ubuntu and the error message is:

make: ***[ksw.o] Error 1

And before that it states:

warning: implicit declaration of function.....

[GenoMax]

You did not post the full error message but in case you are using 32-bit ubuntu this may apply: http://sourceforge.net/p/bio-bwa/[email protected]/

[Superbug]

I am using a 64 bit Ubuntu system!

But the final error message was: make: ***[ksw.o] Error 1

The rest was too many messages, that I can not copy/paste since I am using a VM!

[GenoMax]

Have you allocated more than 4GB RAM for the VM, if you are using 64-bit? Do your error messages look similar to the thread I posted above?

I just compiled latest bwa on a 64-bit ubuntu 14.04 system without problems.

[Superbug]

Yes I have a 64 bit system (just checked again) and also set the Ubuntu Guest to 64 bit.
And I have allocated 1024MB for the VM, as I only have 4GB. Do you think that this is the problem?

[GenoMax]

That could be one explanation.

With just a GB of RAM for the VM you should consider switching to 32-bit ubuntu (though that will cause you other issues if you are working with a non-microbial (largish) genome). In that case it may be better to find other computer resources.

From Ubuntu site:

Ubuntu Desktop 11.04 and up uses Unity as the default GUI while the previous releases used GNOME Panel by default. In order to run Unity the system needs a more capable graphics adapter – see more here or below:

* 1000 ΜHz processor (about Intel Celeron or better)

* 1024 MiB RAM (system memory)

* 3D Acceleration Capable Videocard with at least 256 MB

From experience, we all know that it is recommended to have 2048 MiB RAM to properly run a day to day Ubuntu.

A good start should be with minimum 1024 and recommended 2048 MiB RAM.

[Superbug]

I put it now to 64 bit and 2048MB and do not do anything on my Mac anymore.

But still get the same error message. Also if I leave it at 32bit and 1000MB.

[GenoMax]

Did you get the 32-bit installer for ubuntu and try that or are you using a pre-configured VM?

[Superbug]

Not excactly sure what you mean.... I could change the bit in the VM Setting for my Ubuntu system (Guest).

[GenoMax]

It sounds like you are using OS X as your main OS and then on top of that you are running VM software (virtual box/vmware?) where you are running ubuntu? Is that correct? How are you "changing" from 32-bit to 64-bit?

BTW: If you are using OS X why not compile and use bwa right there? That is a fully qualified BSD-style unix OS.

[Superbug]

Yes that is correct! When I open VirtualBox where I have the VM Ubuntu installed under Settings I can switch from 32 bit to 64 bit and can set how much RAM it can use. This is at least how I understand where I can tell how much the guest can use of the host.
But either way, it was always at 64 bit and most of the things work fine. Only that now I need to use bwa for mapping my reads and during process I encounter problems, where I colleague mentioned that it could be the version of bwa.

[GenoMax]

Why bother with ubuntu when you can use OS X directly? You will need to install Xcode from OS X app store but you should be able to compile bwa on your native OS.

Getting back to the VM: I have a feeling that you are using 32-bit ubuntu (irrespective of what you are setting in the VM settings). Can you post the output of the following command from your ubuntu VM?

$ uname -a

[Superbug]

Because this VM was given to us during a course which has all the necessary scripts and tools that I need to use to analyze my data

This is the output: Linux Pathogens 3.5.0-49-generic #74~precise1-Ubuntu SMP Fri May 2 21:33:28 UTC 2014 i686 i686 i386 GNU/Linux