Convert Plink to Arlequin
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6.1 years ago
HG ▴ 30

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!

software-error plink Arlequin PGDSpider • 3.6k views
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Thanks for your assistance!

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Added plink tag

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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

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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

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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

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

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

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I am using large memory Linux server at my university!

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Okay, please in addition try:

java -d32 -Xmx8G and java -d64 -Xmx8G

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

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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.

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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

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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.

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