help on error 5 (771992)

[Wei Guo]

Hello Tanya,

Sorry to bother you again. I have tried several times but still cannot get past the error.

I have confirmed that my data are in hg19 and lowered the P-value threshold to 1e-5, since my top SNP has a P-value of 6e-6. I was able to successfully obtain the results yesterday. However, after rerunning the PLINK association analysis with a few changes to the phenotype data, I have not been able to get it to work no matter what I try.

When I checked the log file, I noticed that 248,865 SNPs were skipped due to allele mismatch. Should I take any action to address this issue? Could this be the reason I am unable to obtain the results?

Thank you very much for your help.

Best,
Wei

[Tanya Phung]

Hi Wei, 

You specify 1e-5 as the cutoff threshold for p value. The 10 SNPs with the lowest p values in your dataset were all greater than this cutoff threshold, therefore you receive 005 error. You can try again with a higher cutoff threshold: 

awk '{print$6}' topSNPs.txt
p
1.122e-05
1.19e-05
1.611e-05
1.641e-05
1.694e-05
1.716e-05
2.036e-05
3.142e-05
3.625e-05
3.903e-05

Best,

Tanya