CBIIT
Request Timeout (HTTP 408)
Hi I am using LDmatrix in a R script after saving it in .Renviron The script is using LDmatrix in a loop for each chromosome and now it is few days that it is very slow and I got the timeout message after 1-2 iterations.
I tried to change the token after registering a second time but still same error.
Can you please help me to udnerstand? Michela
Hello Michela,
I'm sorry you are experiencing trouble with LDmatrix. I'll do my best to help. Are you receiving the "Request Timeout HTTP (408)"? Do you have your LDlink personal access token stored in .Renviron as an environment variable? If so, as a workaround please try using your access token directly in the LDmatrix function call instead of calling it from .Renviron. See example below:
LDmatrix(snps = c("rs496202", "rs11147477", "rs201578600"), pop = "YRI", r2d = "r2", token = "12xx34567890", genome_build = "grch38" )
Please let me know if this is the problem you're experiencing and if this workaround helps.
If this does not address your problem, we can best help if you provide us with a reproducible example of your code. Include the output of sessionInfo() to give us a summary of your local R environment.
Kind regards, Tim Myers
On Wed, Dec 7, 2022 at 1:42 PM MichelaTr @.***> wrote:
Hi I am using LDmatrix in a R script after saving it in .Renviron The script is using LDmatrix in a loop for each chromosome and now it is few days that it is very slow and I got the timeout message after 1-2 iterations.
I tried to change the token after registering a second time but still same error.
Can you please help me to udnerstand? Michela
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTWARLU5D2BRG7PT5LCCSDWMDLCLANCNFSM6AAAAAASXFKBMU . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hi Tim, Thanks for your quick reply!
I used the token stored in my .Renviron and it worked until last week for most of the chromosomes. Sometimes I got a message that the server was not responsive and I restarted from that iteration and it worked. Maybe connection issues. Now the issue is different. I already tried using the token in LDmatrix function but it is very slow, and it working for 1-3 iterations of my for loop and then I get the timeout message. It looks like the server is slow. (see below)
1] 1 [1] 2
LDlink server is working...
LDlink server is working...
[1] 3
LDlink server is working...
LDlink server is working...
Error in LDmatrix(block_HD_GWAS_SNPs_unique$rsID, pop = "CEU", r2d = "r2", : Request Timeout (HTTP 408).
SessionInfo below and script and an example of the input attached. I don't know why it was working well and now I have this issue.
Thanks!! Best, Michela
[image: Screen Shot 2022-12-07 at 1.23.30 PM.png]
On Wed, Dec 7, 2022 at 12:20 PM Tim Myers @.***> wrote:
Hello Michela,
I'm sorry you are experiencing trouble with LDmatrix. I'll do my best to help. Are you receiving the "Request Timeout HTTP (408)"? Do you have your LDlink personal access token stored in .Renviron as an environment variable? If so, as a workaround please try using your access token directly in the LDmatrix function call instead of calling it from .Renviron. See example below:
LDmatrix(snps = c("rs496202", "rs11147477", "rs201578600"), pop = "YRI", r2d = "r2", token = "12xx34567890", genome_build = "grch38" )
Please let me know if this is the problem you're experiencing and if this workaround helps.
If this does not address your problem, we can best help if you provide us with a reproducible example of your code. Include the output of sessionInfo() to give us a summary of your local R environment.
Kind regards, Tim Myers
On Wed, Dec 7, 2022 at 1:42 PM MichelaTr @.***> wrote:
Hi I am using LDmatrix in a R script after saving it in .Renviron The script is using LDmatrix in a loop for each chromosome and now it is few days that it is very slow and I got the timeout message after 1-2 iterations.
I tried to change the token after registering a second time but still same error.
Can you please help me to udnerstand? Michela
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALTWARLU5D2BRG7PT5LCCSDWMDLCLANCNFSM6AAAAAASXFKBMU
. You are receiving this because you are subscribed to this thread.Message ID: @.***>
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22#issuecomment-1341541274, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOWWGICAX6FW4VK42SLKX3WMDWPNANCNFSM6AAAAAASXFKBMU . You are receiving this because you authored the thread.Message ID: @.***>
Hi Michela,
Could you resend the attachment? I did not receive it for some reason. In the meantime, I'll ask if there could be an issue with the server.
Regards, Tim
On Wed, Dec 7, 2022 at 5:15 PM MichelaTr @.***> wrote:
Hi Tim, Thanks for your quick reply!
I used the token stored in my .Renviron and it worked until last week for most of the chromosomes. Sometimes I got a message that the server was not responsive and I restarted from that iteration and it worked. Maybe connection issues. Now the issue is different. I already tried using the token in LDmatrix function but it is very slow, and it working for 1-3 iterations of my for loop and then I get the timeout message. It looks like the server is slow. (see below)
1] 1 [1] 2
LDlink server is working...
LDlink server is working...
[1] 3
LDlink server is working...
LDlink server is working...
Error in LDmatrix(block_HD_GWAS_SNPs_unique$rsID, pop = "CEU", r2d = "r2", : Request Timeout (HTTP 408).
SessionInfo below and script and an example of the input attached. I don't know why it was working well and now I have this issue.
Thanks!! Best, Michela
[image: Screen Shot 2022-12-07 at 1.23.30 PM.png]
On Wed, Dec 7, 2022 at 12:20 PM Tim Myers @.***> wrote:
Hello Michela,
I'm sorry you are experiencing trouble with LDmatrix. I'll do my best to help. Are you receiving the "Request Timeout HTTP (408)"? Do you have your LDlink personal access token stored in .Renviron as an environment variable? If so, as a workaround please try using your access token directly in the LDmatrix function call instead of calling it from .Renviron. See example below:
LDmatrix(snps = c("rs496202", "rs11147477", "rs201578600"), pop = "YRI", r2d = "r2", token = "12xx34567890", genome_build = "grch38" )
Please let me know if this is the problem you're experiencing and if this workaround helps.
If this does not address your problem, we can best help if you provide us with a reproducible example of your code. Include the output of sessionInfo() to give us a summary of your local R environment.
Kind regards, Tim Myers
On Wed, Dec 7, 2022 at 1:42 PM MichelaTr @.***> wrote:
Hi I am using LDmatrix in a R script after saving it in .Renviron The script is using LDmatrix in a loop for each chromosome and now it is few days that it is very slow and I got the timeout message after 1-2 iterations.
I tried to change the token after registering a second time but still same error.
Can you please help me to udnerstand? Michela
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22, or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ALTWARLU5D2BRG7PT5LCCSDWMDLCLANCNFSM6AAAAAASXFKBMU
. You are receiving this because you are subscribed to this thread.Message ID: @.***>
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22#issuecomment-1341541274, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AVOWWGICAX6FW4VK42SLKX3WMDWPNANCNFSM6AAAAAASXFKBMU
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Thanks!
On Thu, Dec 8, 2022 at 4:36 AM Tim Myers @.***> wrote:
Hi Michela,
Could you resend the attachment? I did not receive it for some reason. In the meantime, I'll ask if there could be an issue with the server.
Regards, Tim
On Wed, Dec 7, 2022 at 5:15 PM MichelaTr @.***> wrote:
Hi Tim, Thanks for your quick reply!
I used the token stored in my .Renviron and it worked until last week for most of the chromosomes. Sometimes I got a message that the server was not responsive and I restarted from that iteration and it worked. Maybe connection issues. Now the issue is different. I already tried using the token in LDmatrix function but it is very slow, and it working for 1-3 iterations of my for loop and then I get the timeout message. It looks like the server is slow. (see below)
1] 1 [1] 2
LDlink server is working...
LDlink server is working...
[1] 3
LDlink server is working...
LDlink server is working...
Error in LDmatrix(block_HD_GWAS_SNPs_unique$rsID, pop = "CEU", r2d = "r2", : Request Timeout (HTTP 408).
SessionInfo below and script and an example of the input attached. I don't know why it was working well and now I have this issue.
Thanks!! Best, Michela
[image: Screen Shot 2022-12-07 at 1.23.30 PM.png]
On Wed, Dec 7, 2022 at 12:20 PM Tim Myers @.***> wrote:
Hello Michela,
I'm sorry you are experiencing trouble with LDmatrix. I'll do my best to help. Are you receiving the "Request Timeout HTTP (408)"? Do you have your LDlink personal access token stored in .Renviron as an environment variable? If so, as a workaround please try using your access token directly in the LDmatrix function call instead of calling it from .Renviron. See example below:
LDmatrix(snps = c("rs496202", "rs11147477", "rs201578600"), pop = "YRI", r2d = "r2", token = "12xx34567890", genome_build = "grch38" )
Please let me know if this is the problem you're experiencing and if this workaround helps.
If this does not address your problem, we can best help if you provide us with a reproducible example of your code. Include the output of sessionInfo() to give us a summary of your local R environment.
Kind regards, Tim Myers
On Wed, Dec 7, 2022 at 1:42 PM MichelaTr @.***> wrote:
Hi I am using LDmatrix in a R script after saving it in .Renviron The script is using LDmatrix in a loop for each chromosome and now it is few days that it is very slow and I got the timeout message after 1-2 iterations.
I tried to change the token after registering a second time but still same error.
Can you please help me to udnerstand? Michela
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22, or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ALTWARLU5D2BRG7PT5LCCSDWMDLCLANCNFSM6AAAAAASXFKBMU
. You are receiving this because you are subscribed to this thread.Message ID: @.***>
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It looks like a server issue at this point. The API server CPU has been close to 100% since Dec 06 due to heavy use of ldproxy by one or more users. Please let us know if you are still having issues. I hope the issue will be resolved soon.
Thanks!
On Thu, Dec 8, 2022 at 11:36 AM Tim Myers @.***> wrote:
It looks like a server issue at this point. The API server CPU has been close to 100% since Dec 06 due to heavy use of ldproxy by one or more users. Please let us know if you are still having issues. I hope the issue will be resolved soon.
— Reply to this email directly, view it on GitHub https://github.com/CBIIT/LDlinkR/issues/22#issuecomment-1343259411, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVOWWGLGYC5TUR4C2O5FUMLWMI2EPANCNFSM6AAAAAASXFKBMU . You are receiving this because you authored the thread.Message ID: @.***>
Hi, I am facing the same issue with using Ldmatrix. Do you have any suggestions to resolve this? Thank you.
Best, Zeal
Also facing the same issue using LDmatrix as well! It tends to work 1 out of every 5-7 attempts.
Thanks, Evin
Thank you both for letting us know. We apologize for the inconvenience. Our team reports that the LDlink API server continues to experience many abnormal requests causing it to run out of resources. These timeout errors are the result. We continue to investigate the issue and look for a resolution. Please stay tuned.
Currently, the LDlink API server is back to normal. Our team will continue to keep a close eye on it.
I also seem to be having issues with the server. My code will work for one or two loops (through chromosomes) before I get the following error:
LDlink server is working...Bad Gateway (HTTP 502)
Is it possible this is an issue on my end? Any suggestions are greatly appreciated!
I ran a few tests of my own and also experienced intermittent issues, including the same 502 error. I contacted our server team and hope to hear back soon. I apologize for the inconvenience.