I assumed it was because for a human sized genome I needed a lot more RAM, so we are using some clusters.
Cheers,
Announcement
Collapse
No announcement yet.
X
-
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.
Leave a comment:
-
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 ;-)Last edited by sklages; 05-10-2013, 04:36 AM.
Leave a comment:
-
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, guysLast edited by JackieBadger; 05-10-2013, 04:27 AM.
Leave a comment:
-
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
Leave a comment:
-
Originally posted by JackieBadger View PostMaybe 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,
Code:ulimit -a
Last edited by sklages; 05-10-2013, 03:58 AM.
Leave a comment:
-
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?
CheersLast edited by JackieBadger; 05-10-2013, 03:12 AM.
Leave a comment:
-
Originally posted by sklages View PostWhat system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)
Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)
Thanks again
Leave a comment:
-
Originally posted by JackieBadger View PostI actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.
I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?
ulimit -a
should give you a hint about that.
Leave a comment:
-
What system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)
Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)
Leave a comment:
-
I actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.
I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?
Leave a comment:
-
In Red Hat/Fedora, it's as simple as "yum install zlib.i386..." I don't use Ubuntu, but as i understand, the installation procedure is similar. This thread says to install ia32-libs to get them. Not having done this on Ubuntu myself, however, I can't offer any more help than that.
Leave a comment:
-
OK...
So I managed to get the program working on my own machine, but the assembly maxed out the RAM (~29GB in a virtual machine). As such I am trying to now install on a linux dedicated machine that has 64GB.
But I am running into problems again.
The installer says I lack the libraries zlib:i386 Lib xi:i386 Lib xtst:i386 and LibXaw:i386
I can not remember how I installed these on my personal cpu a couple of years ago and am now struggling to find a source for these. It seems they are now obsolete??
If I continue with installation and ignore these, I get the following error when atempting to run gsMapper. Any solution for a non-linux boffin would be very much appreciated
"mgplab@new2012:~/454/apps/mapper/bin$ ./gsMapper
Exception in thread "main" java.lang.UnsatisfiedLinkError: /home/mgplab/454/apps/jre/jre1.6.0_30/lib/i386/xawt/libmawt.so: libXi.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.load0(Unknown Source)
at java.lang.System.load(Unknown Source)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.loadLibraries(Unknown Source)
at java.awt.Toolkit.<clinit>(Unknown Source)
at java.awt.Rectangle.<clinit>(Unknown Source)
at com.fourfivefour.ui.Resources.<clinit>(Resources.java:47)
at com.fourfivefour.ui.ResourceFactory.getNewInstance(ResourceFactory.java:79)
at com.fourfivefour.ui.ResourceFactory.get(ResourceFactory.java:66)
at com.fourfivefour.assembly.MapperMain.<clinit>(MapperMain.java:30)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.simontuffs.onejar.Boot.run(Boot.java:340)
at com.simontuffs.onejar.Boot.main(Boot.java:166)
"
Leave a comment:
-
Originally posted by sklages View PostYou don't want to change your login shell, but the system shell:
$ sudo dpkg-reconfigure dash
This is asking you if you want to use 'dash' for '/bin/sh'. Answer 'no' to use 'bash' instead.
hth,
Sven
This worked..and installation completed with no apparent issues.
Appreciate the help guys!
Leave a comment:
Latest Articles
Collapse
-
by seqadmin
At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...-
Channel: Articles
09-26-2023, 06:26 AM -
-
by seqadmin
Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...-
Channel: Articles
09-07-2023, 11:15 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 09-29-2023, 09:38 AM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
09-29-2023, 09:38 AM
|
||
Started by seqadmin, 09-27-2023, 06:57 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
09-27-2023, 06:57 AM
|
||
Started by seqadmin, 09-26-2023, 07:53 AM
|
0 responses
30 views
0 likes
|
Last Post
by seqadmin
09-26-2023, 07:53 AM
|
||
Multiplexed Biomarker Detection with Nanopore Technology: A Leap in Precision Diagnostics
by seqadmin
Started by seqadmin, 09-25-2023, 07:42 AM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
09-25-2023, 07:42 AM
|
Leave a comment: