Haploview error(plz help)

Question

[mmh7272]

Hi i analysis gwas using plink in the linux server and i input plink product map.file and gwas.result by Haploview
But its happen error

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fatal error: Exception in thread "a=AWT-EventQueue-O"java.lang.out.OfMemoryError:GC overhead limit exceeded

can you solve this error directly

plz . help me

[WouterDeCoster]

can you solve this error directly

plz . help me

This will not give your question a higher priority. Rather, if you elaborate on the commands you used, the software versions and the exact circumstances you are more likely to get an accurate answer.

[Kevin Blighe]

You are most likely trying to generate the LD and correlation stats on too many SNPs, which fills up your memory. Try to reduce the SNPs to just the region of interest.

Another tactic: when running JAVA, specify extra initial and max RAM with, for example:

#1024MB starting (1GB); max 8GB
java -Xms1024m -Xmx8g -jar haploview.jar

#256MB starting; max 16GB
java -Xms256m -Xmx16g -jar haploview.jar

[mmh7272]

thank u for ur advise! i use haploview 4.2 however i reduce map file and next step "go to seleted region" click and "go to region"click now appear another error "could not connect to HapMap database" what is problem?

[Kevin Blighe]

I have seen this error before but I cannot remember how I solved it. Can you let me know:

• where you are running haploview - your personal computer or a linux cluster?
• the name of the full path of the file that you are loading

Also, try this: copy the haploview.jar file to where your sample data files are located, and then execute it from there.

The error is very uninformative from the haploview developers.

[mmh7272]

thank u for ur detail advise i try copy the haploview.jar file to where sample data files but same error again

i use linux cluster result file full path : /home/mmh7272/cp/plink292/ger.sand.result.assoc map file full path : /home/mmh7272/cp/plink292/292.map

[Kevin Blighe]

Let me guess: you have no Internet connection via the linux cluster? Can you try to run the program on your personal laptop / desktop? JAVA is portable and can be run in Windows, linux, or Mac

Going by the source code of Haploview, that error message is 'thrown' when there is no Internet connection found

[mmh7272]

Dr. Kevin Blighe i try run personal laptop in windows, but happens same error i just started students in bioinformatics i want ld block anlysis and haplotyping ps . sorry bother you again

[Kevin Blighe]

Hello Sir, so, you are trying to upload via the PLINK Format tab, and, there, you select your results and MAP files.

Regarding the HapMap error, can you go to the HapMap Download tab and de-select the checkbox for Show HapMap info track (see my screenshot, taken just now).

Does that solution the problem?

[mmh7272]

this is my step 1,2 there is nothing when uncheack Show HapMap info track

[mmh7272]

https://ibb.co/mp5sHn https://ibb.co/duY7iS

Answer 1

[Kevin Blighe]

Thanks for sharing. I am guessing that you do have an Internet connection via WiFi or Ethernet (personal laptop)?

I think that you will have to contact the Broad Institute at [e-mail] - there appears to be a general problem.

If you go HERE, for HapMap Download, it mentions GeneCruiser, which for me returns an error: http://genecruiser.broadinstitute.org/genecruiser3/

[mmh7272]

think u for ur advice i really appreciate u ! Cheers! Dr