Error: reading p-value file: no valid p-values found for any SNPs in the data

[Zainab Awada]

Hi,

I am using the following code on Magma: 

  magma --bfile [DATA] --gene-annot [ANNOT].genes.annot --pval [PVAL_FILE] ncol=3

bfile: g1000_eur (downloaded from MAGMA, and used since my pval is derived from europeans)

annot: .genes.annot file (file received after annotation of SNPs using MAGMA)

pval: .txt file with no header and only three columns (col 1: SNP rsid, col 2: P value, col 3: sample size)

My P val file looks like this: 

rs12562373  0.03552  368550
rs1023487  0.277  371339
rs61226122  0.1881  69185
rs60128092  0.89  369660
rs6664873  0.1357  373072

Magma detected three variables in the pval file, but always giving this error: "reading p-value file: no valid p-values found for any SNPs in the data"

Any idea?

   

[Zainab Awada]

I made use of a reply posted on a previous error on this group (although the error was not the same as mine), and will share the solution for others too. There were quotations around snp rsIDs, in both pval file and annotation file (that is generated by MAGMA in the annotation step). When I removed them, the code worked.