Motif discovery issue

[Nicjac]

Hello,

first of all I am very happy I found out about iMotif, I am happy nice
to see such tools appearing on my favorite platform.

I am currently working on a project involving the discovery of
regulatory motifs in various sequences. I tried to use the iMotif
integrated NestedMICA implementation but I get an error message (when
I use the terminal, I get no error when using the GUI, just no result)

hor-camden196:~ nicjac$ /Applications/iMotifs.app/Contents/Resources/
Java/nmica/bin/nminfer -logInterval 100 -out /Users/nicjac/Desktop/
test.xms -numMotifs 5 -minLength 6 -maxLength 9 -expectedUsageFraction
0.500000 -backgroundModel /Users/nicjac/Desktop/test.bg -revComp -
seqs /Users/nicjac/Desktop/test.fasta -maxCycles 100000
Exception in thread "main" java.lang.UnsatisfiedLinkError: /
Applications/iMotifs.app/Contents/Resources/Java/nmica/native/
libnmica.jnilib: no suitable image found. Did find: /Applications/
iMotifs.app/Contents/Resources/Java/nmica/native/libnmica.jnilib: mach-
o, but wrong architecture
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1861)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1778)
at java.lang.Runtime.loadLibrary0(Runtime.java:823)
at java.lang.System.loadLibrary(System.java:1045)
at net.derkholm.nmica.maths.NativeMath.<clinit>(NativeMath.java:34)
at
net.derkholm.nmica.model.BinaryMixPolicy.<init>(BinaryMixPolicy.java:
48)
at net.derkholm.nmica.apps.MotifFinder.main(MotifFinder.java:1078)
at
net.derkholm.nmica.apps.MotifFinderApplication.main(MotifFinderApplication.java:
24)

Any idea how I could fix this issue ? I am using version 0.2.8

Thanks!

Nicolas

[matiasp]

Hi Nicolas

What's the platform you're using iMotifs? Intel 32-bit, Intel 64-bit,
PowerPC? The error message would seem to suggest that NestedMICA's C
library has not been packaged in 0.2.8 for your platform. Sorry!

Best
Matias

[matiasp]

As a quick workaround before we figure out how to resolve this issue,
you can use iMotifs together with a separate NestedMICA installation,
with a terminal, NestedMICA and the iMotifs "Copy to Clipboard"
feature in iMotifs' NestedMICA dialog. You need to replace the
absolute path to the NestedMICA application in the generated command
line string with the path to your own local installation of
NestedMICA.

You can get NestedMICA from here: http://www.sanger.ac.uk/resources/software/nestedmica/

Best
Matias

[Nicjac]

Thanks for the fast reply!

I run iMotif on a Snow Leopard (10.6.2) installation on a Macbook pro.
Obviously this is an intel platform but I am actually unsure if it is
considered 32 or 64 bit. I do not force the 64 bits kernel at boot up
so I guess it is still 32 bits?

Anyway thank you for the workaround!

Regards,

Nicolas

[Matias Piipari]

"About this Mac" (first item in the OS X menu in the upper left corner
of the OS X menu) will tell you.

If your Macbook Pro is fairly old (1st generation of them), it's
processor is a Core Duo which is 32-bit (x86). If it's newer, it'll
have a Core 2 Duo processor, which is 64-bit (x86_64).

I've built iMotifs 0.2.8 with a Core 2 Duo, so my hope would be that
you now respond saying you have a "Core Duo" instead of "Core 2 Duo",
at which point I know exactly how to solve the problem :-)

- - - - - - - - - - -
Matias Piipari
twitter: http://twitter.com/mz2

[Nicjac]

Is it just dependant on the processor ? I have a Core 2 Duo (sorry to
shatter your hopes ;)) but I thought the kernel was still mainly 32-
bit. Anyway hope that helps!

[Matias Piipari]

Hi Nicolas

I think I've got the problem figured out. I'll send a test build for 0.2.9 tomorrow to the mailing list. Would very much appreciate if you could test it on your machine and confirm it fixes the issue.

Matias

[Nicjac]

Excellent, thank you.

Is the file coming up on the web interface of the group as well ? I am
not using the mailing list of the group per-se.

Regards,

Nicolas

[Matias Piipari]

Hi Nicolas

The problem should now be resolved. You should find the NMICA
installation functioning in version 0.3.0. Thanks for reporting the
issue, and let me know if you experience any more problems with
iMotifs! I've added a menu entry to version 0.3.0 that takes you
straight to the project's issue tracker by clicking "iMotifs menu =>
Report an issue / request a feature".

The issue turned out to be the native library linking stage in the
NestedMICA build: although the individual source code files were
compiled as universal binaries which support both 32-bit and 64-bit
Intel and PPC processors, the linker created a dynamic library with
only i386 support included.

Best wishes
Matias

[Nicjac]

Version 0.3.0 works perfectly, thanks again!

Nicolas