Mauve Contig Mover

Question

[HG]

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.

[skymningen]

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.

[HG]

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?

[cts]

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

[HG]

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

[cts]

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

[HG]

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.

[cts]

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

[HG]

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

[HG]

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.

[sa91]

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

[cts]

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

[sa91]

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

[rohitsatyam102]

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.

Answer 1

[cts]

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

[suhalsuhaimi]

hye cts,

the link can't be open