choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
187 stars 90 forks source link

No phenotype presented #238

Closed emiled16 closed 4 years ago

emiled16 commented 4 years ago

I am getting an error when running PRSice. It seems that it is not recognizing the phenotype file. I am getting the following error:

`Phenotype file: pheno.csv
Column Name of Sample ID: FID+IID
Note: If the phenotype file does not contain a header, the
column name will be displayed as the Sample ID which is
expected.

There are a total of 1 phenotype to process

Start performing clumping

Clumping Progress: 100.00%

Number of variant(s) after clumping : 222137

Processing the 1 th phenotype

No phenotype presented

Error:
Execution halted`

I am running the following:

`PRSice_linux

--a1 Effect_allele \
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \
--base IG_stage_1.txt \
--beta  \
--binary-target T \
--bp Position \
--chr Chromosome \
--clump-kb 250kb \
--clump-p 1.000000 \
--clump-r2 0.100000 \
--extract output.valid \
--interval 5e-05 \
--lower 5e-08 \
--num-auto 22 \
--out output \
--pheno pheno.csv \
--pvalue Pvalue \
--seed 3170507045 \
--snp MarkerName \
--stat Beta \
--target c_imp.QC.FINAL \
--thread 1 \
--upper 0.5`

Here is the first few lines of my phenotype file:

FID IID pheno 4 4 0.0 5 5 0.0 6 6 0.0 7 7 0.0 8 8 0.0 9 9 0.0 10 10 0.0 11 11 0.0 12 12 0.0

Everything looks good, I don't know why this error is popping? Thanks in advance

emiled16 commented 4 years ago

It worked! I changed the type of the pheno column to integer.