Plotting error: Error in names(x) <- value : 'names' attribute [4] must be the same length as the vector [2]

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Nora Strom

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Jul 28, 2021, 12:02:28 PM7/28/21

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Hi,

unfortunately, I have been running into the same error over and over again (see my terminal output below) and I can't seem to figure out what is causing the issue. When not including any covariates it runs through just fine. This might be obvious and it might be that I am overlooking something. But do you have any idea what might cause this?

Thanks a lot, Nora

PRSice 2.3.3 (2020-08-05)

https://github.com/choishingwan/PRSice

GNU General Public License v3

If you use PRSice in any published work, please cite:

Choi SW, O'Reilly PF.

PRSice-2: Polygenic Risk Score Software for Biobank-Scale Data.

GigaScience 8, no. 7 (July 1, 2019)

2021-07-28 17:17:43

./PRSice_linux \

--a1 A1 \

--a2 A2 \

--all-score \

--bar-levels 5e-07,1e-06,0.0001,0.001,0.01,0.05,0.1,0.2,0.5,1 \

--base daner_OCS_LOO_woSWE_270521_Beta \

--base-info INFO:0.8 \

--base-maf FRQ_A_17055:0.01 \

--binary-target F \

--bp BP \

--chr CHR \

--clump-kb 250kb \

--clump-p 1.000000 \

--clump-r2 0.100000 \

--cov covariates_YATSS_GSA_age_agesq_10PCs_SEX_BATCHES_recoded_outliersremoved.qcovar \

--cov-col AGE,AGESQ,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,SEX,BATCH_recoded \

--cov-factor SEX,BATCH_recoded \

--fastscore \

--num-auto 22 \

--out OCS_LOO_SWE_Yatss_PRSice2_wcov_28.07.21 \

--perm 10000 \

--pheno Pheno_YATSS_onlyGWASIDs_header_unrelated \

--pvalue P \

--score std \

--seed 152134272 \

--snp SNP \

--stat BETA \

--target Yatss_GSA_hm3_geno0.01_maf0.03_chr1-22 \

--thread 1

Initializing Genotype file:

Yatss_GSA_hm3_geno0.01_maf0.03_chr1-22

(bed)

Start processing daner_OCS_LOO_woSWE_270521_Beta

==================================================

Base file: daner_OCS_LOO_woSWE_270521_Beta

Header of file is:

CHR SNP BP A1 A2 FRQ_A_17055 FRQ_U_17055 INFO BETA SE P ngt

Direction HetISqt HetDf HetPVa Nca Nco Neff_half

Reading 100.00%

5935197 variant(s) observed in base file, with:

41 NA stat/p-value observed

794803 ambiguous variant(s) excluded

5140353 total variant(s) included from base file

Loading Genotype info from target

==================================================

3358 people (0 male(s), 0 female(s)) observed

3358 founder(s) included

95929 variant(s) not found in previous data

13 variant(s) with mismatch information

995809 variant(s) included

Phenotype file:

Pheno_YATSS_onlyGWASIDs_header_unrelated

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 : 83838

Processing the 1 th phenotype

OCS_Zscore is a continuous phenotype

1311 sample(s) without phenotype

2047 sample(s) with valid phenotype

Processing the covariate file:

covariates_YATSS_GSA_age_agesq_10PCs_SEX_BATCHES_recoded_outliersremoved.qcovar

==============================

Include Covariates:

Name Missing Number of levels

AGE 0 -

AGESQ 0 -

PC1 0 -

PC2 0 -

PC3 0 -

PC4 0 -

PC5 0 -

PC6 0 -

PC7 0 -

PC8 0 -

PC9 0 -

PC10 0 -

SEX 0 2

BATCH_recoded 0 2

After reading the covariate file, 2047 sample(s) included

in the analysis

Start Processing

Processing 100.00%

There are 1 region(s) with p-value between 0.1 and 1e-5

( [1;31mmay not be significant [0m).

Begin plotting

Current Rscript version = 2.3.3

Error in names(x) <- value :

'names' attribute [4] must be the same length as the vector [2]

Calls: colnames<-

Execution halted

srun: error: sens2019017-b9: task 0: Exited with exit code 1

Nora Strom

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Aug 4, 2021, 6:23:31 AM8/4/21

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Hi,

I just found the same issue on the PRSice github page (https://github.com/choishingwan/PRSice/issues/261#issuecomment-789004512).