error in generation of the velvet_asm.afg file

[akshaya.ramesh]

Hello,

I have been working on de-novo genome assembly using the Velvet algorithm. Of the 10,000 contigs generated in my contigs.fasta file, the .afg file generated at by Velvet contains only information for the first 4,000 contigs. I do have plenty of storage left and I am not exactly sure as to what is going on. Has anyone else run into a similar problem or do you guys have any thoughts on this?

Thank you for your time.

Akshaya

[mastal]

error in generation of the velvet_asm.afg file

Are your contigs ordered by size, is it cutting out the smaller ones for some reason?

I had a lot of problems generating velvet .afg files when I was using a desktop computer that kept running out of memory, I haven't had any more problems since I've been working with smaller files and a more powerful computer.

[akshaya.ramesh]

Thank you so much for getting back to me.
My contigs are ordered by size, from the smallest to largest. It cuts off contigs that are larger in size (all contigs above 20,000 bp are cut-off). I have been using Tablet (http://bioinf.scri.ac.uk/tablet/download.shtml) to view my .afg files. I assumed that there might be an issue with the memory as well, however I do not receive any error message (I received an error message earlier when I ran out of memory with my .afg files).
I am using a desktop computer as well, I will try using a more powerful computer. Also, could you tell me what program you were/are using to view your .afg files?

[mastal]

error in generation of the velvet asm.afg file

I was using Tablet too, and having to make .afg files for individual contigs because it kept running out of memory. I then tried using Hawkeye.

[akshaya.ramesh]

I was using Tablet too, and having to make .afg files for individual contigs because it kept running out of memory. I then tried using Hawkeye.

Thank you so much for the suggestion. It took me a while to install qt4 and AMOS. when I try to open my file using hawkeye, I get a error message saying

cannot connect to X server

Did you ever run into this problem/know what is going on?

Thanks again,
Akshaya

[ewilbanks]

where are you running hawkeye from? If you're running this from a machine that you have ssh'ed into - you need to login like this:

ssh -X [email protected]

Hawkeye is trying to launch the GUI and running into an issue with (I think) the X11 server. And man do I feel you about the issues getting qt4 and AMOS installed... phew! just did that...

[akshaya.ramesh]

I did not have xming installed on my system. Its working now. Thank you.