Question: Convert Plink to Arlequin
0
gravatar for HG
2.6 years ago by
HG30
HG30 wrote:

I am looking for a software to convert PLINK file (large!) to the Arlequin format.I have used PGDSpider but I got the following error: ERROR 06:09:40 - not enough memory. To increase the allowed memory see help. Is there any other method to do that? Thanks in advance!

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by HG30
1

Thanks for your assistance!

ADD REPLYlink written 2.6 years ago by HG30

Added plink tag

ADD REPLYlink written 2.6 years ago by Kevin Blighe67k

There is minimal support for Arlequin on this website. I have looked and there are many unanswered questions related to the program. I also checked the Arlequin manual and it does not support PLINK data files.

it also seems that the developers themselves have 'packed up shop' - the last edit on their Home Page was from 2015, and their support forum no longer exists.

Kevin

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Kevin Blighe67k
1

Run the program from the command prompt and add the -Xmx command line parameter:

java -Xmx8G -jar PGDSpider.jar #8 gigabytes RAM

You can also do this via point-and-click: https://ximacare.ximasoftware.com/hc/en-us/articles/204507235-Increasing-Java-Memory-Limits

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Kevin Blighe67k
1

Thanks Kevin.It worked and I could change data from plink to Arlequin. Although I got another error in Arlequin: [1]+ Segmentation fault (core dumped) nohup ./arlecore3522_64bit Do you have any idea? Thanks in advance

ADD REPLYlink written 2.6 years ago by HG30

What is your laptop spec and has it a 32- or 64-bit bus?

You may try to increase RAM further, if you wish.

ADD REPLYlink written 2.6 years ago by Kevin Blighe67k

I am using large memory Linux server at my university!

ADD REPLYlink written 2.6 years ago by HG30

Okay, please in addition try:

java -d32 -Xmx8G and java -d64 -Xmx8G

Also, please mention the version of Java installed by your system administrator.

ADD REPLYlink written 2.6 years ago by Kevin Blighe67k

Kevin, as I mentioned I have done with PGDSpider using java -Xmx8G, I could get the output. Now my problem comes up when I use Arlequin as the following error: [1]+ Segmentation fault (core dumped) nohup ./arlecore3522_64bit. Thanks.

ADD REPLYlink written 2.6 years ago by HG30
1

It is yet another issue with RAM. So, just like we increased RAM for the JAVA command, we have to increase it for whatever command you are now running. The way to do this will depend on which OS is installed on the server. For assistance, you may have to contact the system administrator

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Kevin Blighe67k
1

I'd also recommend using the -Xms option and setting it to 8G as well. That'll make sure your program only starts when 8G of memory is allocated to it.

ADD REPLYlink written 2.6 years ago by RamRS30k
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