Mauve Contig Mover
1
1
Entering edit mode
8.4 years ago
HG ★ 1.1k

Dear all, Currently i am using "Mauve contig mover" to make an ordering of contig. I have one contig file (around 200 contig) and one reference genome file. When i am using GUI based upload its working fine. Can anybody please let me know how to use in command line.

Thank you all.

• 7.5k views
ADD COMMENT
0
Entering edit mode

The contig mover only uses the normal progressive_mauve command. It is no singular tool, but uses iterative runs of progressive_mauve (or the old mauve, I am not completely sure) to get the contig order that includes the least rearrangements in comparison to the reference. Edit: What I meant to say is: there is no command line tool for it. The functionality is somewhere hidden in Mauve.jar.

ADD REPLY
0
Entering edit mode

For progressive mauve i used this command ./progressiveMauve --output=twoway.xmfa --output-guide-tree=twoway.tree --backbone-output=twoway.backbone sequence.fasta Ecoli-1_out.2.unpadded.fasta

Could you please modify my command to iterative runs?

ADD REPLY
0
Entering edit mode

Not true, the functionality is not hidden from the user, see my answer below for instructions

ADD REPLY
0
Entering edit mode

I already tried with this command: java -Xmx500m -cp/home/hiren/Desktop/mauve/mauve1 Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref sequence.fasta -draft Ecoli-1_out.unpadded.fasta

But i did not get any satisfactory out put

Error like that:

Exception in thread "main" java.lang.NoClassDefFoundError: Mauve/jar Caused by: java.lang.ClassNotFoundException: Mauve.jar at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: Mauve.jar. Program will exit

Regards

Hiren

ADD REPLY
0
Entering edit mode

Could that error be with your command. In the one you give above there is a spacer between mauve1 and Mauve.jar but I don't hink that should be the case. I can replicate your error on my computer by putting in a space in the path. see my 'fixed' version of your command below and try it out to see if it works

java -Xmx500m -cp/home/hiren/Desktop/mauve/mauve1/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref sequence.fasta -draft Ecoli-1_out.unpadded.fasta

ADD REPLY
0
Entering edit mode

Hi cts thanks for suggestion but i am sorry to say still there is some error can you please check it once

hiren@FB11-10207:~/Desktop/mauve/mauve1$ java -Xmx500m -cp /home/hiren/Desktop/mauve/mauve1/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref sequence.fasta -draft Ecoli-1_out.unpadded.fasta Exception in thread "main" java.lang.NoClassDefFoundError: org/gel/mauve/contigs/ContigOrderer Caused by: java.lang.ClassNotFoundException: org.gel.mauve.contigs.ContigOrderer at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) Could not find the main class: org.gel.mauve.contigs.ContigOrderer. Program will exit.

ADD REPLY
0
Entering edit mode

That's strange. I'm going to fall back to the tried and true response of "what version are you using?". I downloaded a mauve snapshot from this website to test things out: http://gel.ahabs.wisc.edu/mauve/source/snapshots/

perhaps there is a difference between this development version

ADD REPLY
0
Entering edit mode

Thanks CTS for suggestion its working properly now......

ADD REPLY
0
Entering edit mode

Hey cts i have another question once i am running mauve contig mover i am getting n number iteration and for each time mauve generate one folder name alignment1, alignment2 and so on. Now i want only final iteration result, from command line after running mauve how i will automatically go to that folder and save the result another result folder.

ADD REPLY
0
Entering edit mode

I've encountered a similar problem and I was wondering if you could help me. I downloaded Mauve 2.3.1 to the Applications/Mauve-2.3.1 directory. I'm running Mac OS X 10.6.8, and java version "1.6.0_51" Java(TM) SE Runtime Environment (build 1.6.0_51-b11-457-10M4509) Java HotSpot(TM) 64-Bit Server VM (build 20.51-b01-457, mixed mode)

I tried to use the mauve contig mover from the command line following the user's guide by typing: java -Xmx500m -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft batch1_assembly_1.fasta

I'm getting the following error: Error running aligner. java.io.IOException: Cannot run program "progressiveMauve": error=2, No such file or directory at java.lang.ProcessBuilder.processException(ProcessBuilder.java:478) at java.lang.ProcessBuilder.start(ProcessBuilder.java:457) at java.lang.Runtime.exec(Runtime.java:593) at java.lang.Runtime.exec(Runtime.java:466) at org.gel.mauve.gui.AlignWorker.construct(Unknown Source) at org.gel.mauve.gui.SwingWorker$2.run(Unknown Source) at java.lang.Thread.run(Thread.java:680) Caused by: java.io.IOException: error=2, No such file or directory at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.<init>(UNIXProcess.java:53) at java.lang.ProcessImpl.start(ProcessImpl.java:91) at java.lang.ProcessBuilder.start(ProcessBuilder.java:452) ... 5 more

I also downloaded a mauve snapshot following the link suggested by cts above, but none of the commands I tried worked. Thanks, Silvia

ADD REPLY
0
Entering edit mode

I'm not sure what has caused this error. You could try sending it through the mauve mailing list of emailing the maintainer directly. They will probably have a better idea of what's happening

ADD REPLY
0
Entering edit mode

Thank you. I found something useful in the archives of the [Mauve-users] list that I hadn't seen before.

I added /Applications/Mauve-2.3.1//Mauve.app/Contents/MacOS to my $PATH.

Then from a directory containing the reference genome and the draft genome I ran the following command: java -Xmx500m -cp /Applications/Mauve-2.3.1/Mauve.app/Contents/Resources/Java/Mauve.jar org.gel.mauve.contigs.ContigOrderer -output batch1_assembly_1_mcm -ref LrGG.fasta -draft batch1_assembly_1.fasta

That worked. Posting here in case it helps someone else in the future.

Silvia

ADD REPLY
0
Entering edit mode

Hi!! I ran Mauve Contig Mover and I have multiple folders. Which one should I choose? The final one? I am inquiring this because in my first iteration I don't get any contig enlisted as conflicting ordering. However, in my final alignment, there are 18 contigs out of 96 that are marked as conflicting ordering. Should I consider an assembly with zero conflicting contig order or should I still use the last iteration? Please guide me.

ADD REPLY
0
Entering edit mode
8.4 years ago
cts ★ 1.6k

see this page which describes how to access the mauve contig mover from the command-line

ADD COMMENT
0
Entering edit mode

hye cts,

the link can't be open

ADD REPLY

Login before adding your answer.

Traffic: 2368 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6