Internal server error

[sarita 693]

Dear Sir 

I am trying to generate locus zoom plot , but it is creating QQ plot, manhattan plot complete but unable to generate locuszoom plot. It start to create locuszoom and labels genes name on x-axis but after this it does not show any variants and shows internal server error. 

 kindly help me in troubleshooting this.  I would be very thankful to you.

[sarita 693]

I am using online tool.

[Andrew Boughton]

Thanks for the question. The basic site appears to be working. Perhaps there is something odd with this specific dataset? If you send me an email privately off list with a link, I can take a look.

(The site has a feature to share private datasets via special links, which may be of use)

-Andy Boughton

abo...@umich.edu

On Jul 7, 2023, at 3:22 AM, sarita 693 <saritat...@gmail.com> wrote:

Dear Sir 

I am trying to generate locus zoom plot , but it is creating QQ plot, manhattan plot complete but unable to generate locuszoom plot. It start to create locuszoom and labels genes name on x-axis but after this it does not show any variants and shows internal server error. 

 kindly help me in troubleshooting this.  I would be very thankful to you.

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[camj...@gmail.com]

Dear Sir,

 

I am currently using on the Linux Cluster System and trying to generate LocusZoom plots. Below is the command am using:

 

~/locuszoom/bin/locuszoom --metal EPI_LOW3.EA.chr10.4230494.G.A.csv --delim , --markercol snp --pvalcol fixed.p --source 1000G_Nov2014 --build hg38 --pop EUR --hitspec EPI3.locusZoom_chr10.4230494.G.A.txt --no-cleanup --plotonly --prefix ALL

 

module load python/2.7.9

module load R/3.6.1

module load rstudio

 

snp chr start end flank run m2zargs

10:4240181 10 NA NA 500kb yes title="EA" signifLine=7.3 signifLineColor=red ymax=10

 

I can obtain the LocusZoom Plot but without the LD Coloring and Recombination. Below is the error message I keep getting:

 

Creating new LD cache branch for current LD source/population/build..

Error: PLINK did not complete successfully. Please check the log file (run with --no-cleanup to see the directory with the log file.)

Warning: LD could not be computed for SNP 10:4240181. This SNP does not exist in the genotype files for computing LD from 1000G_Nov2014/hg38/EUR..

Warning: recombination rate table 'recomb_rate' not found in database, skipping recomb rate lookups in region

Read 7 items

Warning message:

No usable LD information.

trans signif line at: 7.3

 

Even though this SNP is present in the Chr10.bim file but I keep getting the error message. Am fine with having just the LD Coloring and without the Recombination. Please let me know if there is any help you can provide.

 

Kind Regards,

Julius