How to expand memory for TASSEL or work with large data sets

[Jordon Pace]

Hi,

I am a new user of TASSEL and am trying to work with a very large GBS data set. I have raw and imputes Genotype by Sequencing data for 384 maize inbred lines across all 10 chromosomes. I try to run any kind of analysis and I always get a notice that the matrix is too large. How do I get around this? I have heard you can expand the memory but I can't figure it out based just on what I find in the tutorial (I don't have a ton of programming or script writing abilities). If anyone can help that would be great. 

Thanks for your time,

Jordon Pace

[Terry Casstevens]

Hi Jordon,

Add this flag...

./run_pipeline.pl -Xmx5g

Where example 5g specifies 5GB of memory.

Cheers,

Terry

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[Jordon Pace]

Hi Terry,

I want to thank you for your help. I am wondering. Where do I add the flag you posted? Do I need to do it with Perl or would just notepad work? I pretty much have no experience (other than a little work with R) in coding. 

Jordon

[Terry Casstevens]

Hi Jordon,

There is no coding needed. Add that flag to the beginning just as I
typed. What tutorial document are you using?

Cheers,

Terry

> https://groups.google.com/d/msg/tassel/-/MKly655RX0QJ.

[Jordon Pace]

http://cbsu.tc.cornell.edu/lab/doc/TASSEL_20120214.pdf, that's the website with the tutorial. So I just add the plugin to the start_tassel.bat?

Jordon

[Jordon Pace]

Maybe it would be best to just tell you where I am. I am trying to analyze GBS data with over 700,000 SNPs over the 10 maize chromosomes of 384 lines. Anytime I really try and do anything at all I get an error message "matrix too large" something like that. I am just wondering how I can manipulate TASSEL so that I can proceed with my project. I have Tassel 3.0 standalone and am using a Windows 7 PC. If you have any advice on that. That would be awesome.

Again, thank you for your time,

Jordon

[Terry Casstevens]

Hi Jordon,

It would be easier to diagnose your problem if you send the command
and error messages copied directly from your console. Try editing
start_tassel.bat (which I presume you are running?) and change the
-Xmx flag to have a bigger number. For example -Xmx5g

Terry

> https://groups.google.com/d/msg/tassel/-/zea_O5kSd2AJ.

[Iván barrero]

Have you try using GAPIT?

Are you sure you increase your workspace size?

It is my understanding that GAPIT is more efficient than tassel to analyze large datasets

You can download from buckler's lab

Once again, make sure to increase your workspace in R ( GAPIT run in R)

Best regards

Sent from my iPhone

To view this discussion on the web visit https://groups.google.com/d/msg/tassel/-/zea_O5kSd2AJ.

[Jordon Pace]

Ok, I have uploaded my Chromosome 1 data into TASSEL and click the LD button. Message I get after clicking the sliding window is "Unable to run Linkage Disequilibrium Matrix too large". I also have tried opening the start_tassel.bat with notepad and made the changes you have put and it still gives the message previously noted.

Jordon

[Jordon Pace]

I am not if I have increased the work space size or not, is there a way to make sure? I also have heard of GAPIT but am not sure that it will do everything I want to do at this point.

Thanks,