Comments (8)
Update: after 10 minutes or so it does produce a plot! But during that time R is completely frozen and can't be interrupted, only force killed. Does it download or compute full 1000 genomes LD data each time or something?
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Hi Jeremy37
How do you solve the problem? I got the same problem in my linux server. Is the MySQL server still alive?
Failed to connect to database: Error: Can't connect to MySQL server on 'locuscompare-us-west-2a.cvocub39nnri.us-west-2.rds.amazonaws.com' (110)
Thanks.
from locuscomparer.
HI,
I have the same Issue. I run the example but I only get the plot only contain the variant rs9349379
on each of the 3 plots. I am running this on a Linux cluster. R version 3.4.4
Thank you
devtools::session_info()
Session info ------------------------------------------------------------------
setting value
version R version 3.4.4 RC (2018-03-09 r74376)
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz US/Eastern
date 2019-07-05
from locuscomparer.
Hello @Jeremy37 @Huang-Ying @cvalenci. Thank for reaching out.
I cannot reproduce this error on my own laptop or my server.
It seems like this issue relates to AWS connectivity. One possibility is that Amazon restricts bandwidth or similar on a region-by-region basis. Could you provide me with your rough geographic location (i.e. New York, Florida) and I can VPN into that region to see what's going on?
from locuscomparer.
Hi,
Sure, I am located at Baltimore, Maryland.
from locuscomparer.
I tried VPNing into multiple locations (Canada, UK, Brazil, Australia) and they all worked fine. So far, I cannot reproduce this error.
However, I do believe this issue needs to be addressed. I recently had a friend who complained that her work computer cannot access locuscompare, but when she tried to run the same command at home, it worked. So one thing I definitely recommend is to try multiple points of connection. I know this is probably the worst advice and I do apologize for that.
@Jeremy37 To answer your question, locuscomparer is designed to only retrieve LD information it needs. This mean very little memory footprint and, in theory, should only take a few seconds in most cases (5000 SNPs or less). It is strange it would take 10 minutes.
from locuscomparer.
I think that it might a sporadic connection issue. I've run it on our servers, and one day it fails, and the next it works. A bit mysterious.
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Glad it worked for you :)
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Related Issues (20)
- Points sometimes don't color correctly HOT 1
- Fail to connect to database HOT 3
- Change source for LD computation
- error in code for example(get_lead_snp)
- Error while running locuscomparer HOT 2
- a problem about legend HOT 1
- How could I add a main title for the figure?
- How can I change Y axes HOT 1
- I can not open the link: http://locuscompare.com/ HOT 6
- How to incorporate own LD instead of reference LD?
- Failed to connect to database: Error: Can't connect to MySQL server on 'locuscompare-us-west-2a.cvocub39nnri.us-west-2.rds.amazonaws.com' (111)
- Problems with plotting extreme small P-values
- Error with RMySQL
- SNPs of locuscomparer are not the same as colocalization SNPs HOT 3
- Top SNP level is not showing for GWAS plot HOT 1
- locuscompare HOT 2
- locuscompare
- No connection to MySQL server
- Fail to connection to server during query
- Wrong SNP being assigned purple colour
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