Installing Newbler 2.7 on Ubuntu 12.04, java problem

[JackieBadger]

I edited the start up scripts to point in the direction of the new Oracle Java executable, and it seems to initially work.

The GUI looks to start up, with the picture of the 454 machine and "starting...".... but then dissapears without crashing out in the terminal. So the terminal still indicates the program is running but no GUI.

Maybe it is due to the Java version, java/jdk1.7.0_21?
Any ideas?

Cheers

[sklages]

Maybe it is due to the Java version, java/jdk1.7.0_21?
Any ideas?

Cheers

Yes, it is. Do not use Java 7 with the Roche suite, instead go for 6.

Nevertheless, don't forget to check if there are any limts on your machine,

ulimit -a

should help ..

[JackieBadger]

Thanks a lot, guys. Its all up and running now.
ulimit -a shows no limits on the machine on the machine with the new installation.

Thanks again

[JackieBadger]

OK so I got the memory crash again on the more powerful machine.

Here is the ulimit -a output:

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 514997
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 514997
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited


My reference file is a genome scaffold consiting of 2,962,365 contigs; 1,555,444,314 bp

My query sequences consit of 1,151,700 contigs: 390,436,936 bp
It is after the Index/screening of my query sequences where the compuation runs out of memory.
On both machines (29GB, and 62GB available respectivly) mapping crashes when it uses a little over 50% of the available RAM

ANy ideas how to remedy?
Maybe I should cut my refernce file in half?

THanks again, guys

[sklages]

Seems gsmapper wants to use more than 64GB RAM .. well, it's a "heavy" reference ...
Just take a few thousands of the largest contigs (is it a cDNA backbone?) and try again, just to see if the installation itself is OK (it probably is).

Finally you need to reduce your reference contigs or look for a more powerful machine.

Just curious, why do you want to map many, many contigs on even more many, many contigs? Maybe you should look for another software to achieve the results you are expecting?

EDIT: Oh, I haven't noticed your 50% issue. Maybe you should contact your sysadm about that. It is worth a try ;-)

[JackieBadger]

Thanks. WIll do.

The reference is a genome of a closely related species to the cDNA query sequencs I have (poly A/T trimmed).
So I want to use the reference to essential construct ESTs and look for SNPs.
De Novo EST assembly works fine, although it seems intuative to use a reference where possible.

[sklages]

Have you solved your "50% problem"?

[JackieBadger]

I assumed it was because for a human sized genome I needed a lot more RAM, so we are using some clusters.
Cheers,