[BUG]: Server code: 503; Server is possibly experiencing traffic, trying again...

[AStudentShen]

Hello everyone I am trying to use the function 'clump_data' with the R package 'TwoSampleMR'.However, I find that this problem happens with some data. The problem is that Server code: 503; Server is possibly experiencing traffic, trying again... As an example this one causes an error:Clumping ohKmwJ, 64 variants, using EAS population reference Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again... Server error: 503 Failed to retrieve results from server. See error status message in the returned object and contact the developers if the problem persists.

What would be the reason of this problem? Thank you.

[llalluan]

Hi， I am experiencing the same issue when running the clump_data when i have data with 2 SNPs, but when I changing the other data, i works. But I don't know why.

[AStudentShen]

Hi， I am experiencing the same issue when running the clump_data when i have data with 2 SNPs, but when I changing the other data, i works. But I don't know why.

I think the reason of that is about Internet. U can try to use clump_local_data with R package 'ieugwasr' to instead this function.

[llalluan]

Hi， I am experiencing the same issue when running the clump_data when i have data with 2 SNPs, but when I changing the other data, i works. But I don't know why.

I think the reason of that is about Internet. U can try to use clump_local_data with R package 'ieugwasr' to instead this function.

I have tested the Internet by changing testing data several times, but it seems none of the internet's business. The issue just happened when performing with the specific data, but I didn't the difference between them, so I guess the reason for that is might about the reference panel, it doesn't contain those specific SNPs.

[skyer111]

I have also encountered this problem.It seems to be related to some specific SNPs? I guess

[daydayfei]

我也遇到了，我的问题snp是下面的两个 1	6	32359880	T	C	1.3240	0.2409	0.0057	3.868e-08	9363	rs117587844	exposure	TRUE	reported	Hexadecenoylcarnitine
2	11	36373290	A	G	-0.5269	0.0965	0.9805	4.775e-08	9363	rs180686060	exposure	TRUE	reported	Hexadecenoylcarnitine

exp_online_ld <-clump_data(exp_pro,clump_r2=0.001,clump_kb=10000) Please look at vignettes for options on running this locally if you need to run many instances of this command. Clumping Hexadecenoylcarnitine, 2 variants, using EUR population reference Server code: 503; Server is possibly experiencing traffic, trying again... Server code: 503; Server is possibly experiencing traffic, trying again...

使用本地clump_local方法报RT错误 PLINK v1.90b7.2 64-bit (11 Dec 2023) www.cog-genomics.org/plink/1.9/ (C) 2005-2023 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to C:\Users\10718\AppData\Local\Temp\RtmpkrWZxz\file84206c8c606c.log. Options in effect: --bfile E:/Environment/LDREF/EUR --clump C:\Users\10718\AppData\Local\Temp\RtmpkrWZxz\file84206c8c606c --clump-kb 10000 --clump-p1 1 --clump-r2 0.001 --out C:\Users\10718\AppData\Local\Temp\RtmpkrWZxz\file84206c8c606c

32452 MB RAM detected; reserving 16226 MB for main workspace. 8550156 variants loaded from .bim file. 503 people (0 males, 0 females, 503 ambiguous) loaded from .fam. Ambiguous sex IDs written to C:\Users\10718\AppData\Local\Temp\RtmpkrWZxz\file84206c8c606c.nosex . Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 503 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is in [0.9999995, 1). 8550156 variants and 503 people pass filters and QC. Note: No phenotypes present. Warning: No significant --clump results. Skipping. 错误于file(file, "rt"): 无法打开链结 此外: 警告信息: In file(file, "rt") : 无法打开文件'C:\Users\10718\AppData\Local\Temp\RtmpkrWZxz\file84206c8c606c.clumped': No such file or directory 也就是说本地和在线都出错