Proxy CONNECT aborted due to timeout

[ZoheirAlayash]

Hello,

I am conducting a series of cis-mendelian randomization analyses for a number of proteins and an outcome. In some cases I have SNPs that are missing from the outcome genome-wide association study (GWAS). Thus, I am aiming to replace the missing SNPs with proxies that are found in the both GWAS.
Even when I tried the function for one SNP, the process was aborted.
my_proxies <- LDproxy(snp = "rs79251236", pop = "CEU", r2d = "r2", token="MyToken" genome_build = "grch37", win_size = 500000 ) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [ldlink.nih.gov] Proxy CONNECT aborted due to timeout
I wanted to know if there is a server issue that is behind my error or if I am doing something wrong? Also, I got around 2500 proteins that has missing SNPs in the outcome, so I have to heavily use LDproxy. Do you have any recommendations on how to run LDproxy several times without causing trouble for users?

[timyers]

Hi,

Are you still experiencing a problem? I tried your code example above and did not get the same timeout error. Sometimes when the server is scaled out, it may need a brief time to warm-up. This could cause time-out errors for some requests. I suppose there could also be a network connection issue. If the problem persists, please post here again to let us know.

As to your second question, please give the LDproxy_batch function a try to see if it can handle the size of your SNP list.
If not, please let us know.

Tim