PRSice "command not found"

Question

[aredha2]

Hi all, When running PRSice (version 2.3.3), I got the "command not found" for the commands: --perm --thread --binary-target T

How to make these commands working. Best regards, Redha

[Sam]

I'll need to see the full log to know what's going on.

Answer 1

[aredha2]

Hi Sam, Please see below the log. As you can see many commands have been mentioned as not found. Even when I run the script with the command "--pheno-col" (in another run not reported in my present message), the command does not work. Best reagrds, Redha

(base) [redhaa@opti ~]$ cd /share/experimentdb/ExperimentDB/2021/Redha/PRSIce_folders/PRSice_linux/ (base) [redhaa@opti PRSice_linux]$ (base) [redhaa@opti PRSice_linux]$ Rscript PRSice.R --dir . \

--prsice ./PRSice_linux \
--base GWAS_tab.txt \
--snp snp --chr chromosome --bp position --A1 a1 --A2 a2 --pvalue p_metal --stat or \
--extract PRSice.valid \
--target target_files \
--pheno /share/experimentdb/ExperimentDB/2021/Redha/PRSIce_folders/PRSice_linux/Phenotypes_ADVANCE/phenotype_tab.pheno

PRSice 2.3.3 (2020-08-05) https://github.com/choishingwan/PRSice (C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O'Reilly 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) 2021-08-27 06:00:49 ./PRSice_linux \ --a1 a1 \ --a2 a2 \ --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 \ --base GWAS_tab.txt \ --binary-target T \ --bp position \ --chr chromosome \ --clump-kb 250kb \ --clump-p 1.000000 \ --clump-r2 0.100000 \ --extract PRSice.valid \ --interval 5e-05 \ --lower 5e-08 \ --num-auto 22 \ --or \ --out PRSice \ --pheno /share/experimentdb/ExperimentDB/2021/Redha/PRSIce_folders/PRSice_linux/Phenotypes_ADVANCE/phenotype_tab.pheno \ --pvalue p_metal \ --seed 2008959332 \ --snp snp \ --stat or \ --target target_files \
--thread 1 \
--upper 0.5

Initializing Genotype file: target_files (bed)

Start processing

GWAS_tab

SNP extraction/exclusion list contains 5 columns, will assume first column contains the SNP ID

Base file: GWAS_tab.txt Header of file is: snp chromosome position a1 a2 or p_metal

Reading 100.00% 5864396 variant(s) observed in base file, with: 2011473 variant(s) excluded based on user input 3852923 total variant(s) included from base file

Loading Genotype info from target

4098 people (2574 male(s), 1524 female(s)) observed 4098 founder(s) included

2788357 variant(s) not found in previous data 17 variant(s) with mismatch information 3806767 variant(s) included

Phenotype file: /share/experimentdb/ExperimentDB/2021/Redha/PRSIce_folders/PRSice_linux/Phenotypes_ADVANCE/phenotype_tab.pheno 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 : 104890

Processing the 1 th phenotype

"stroke_tot" is a binary phenotype 3633 control(s) 465 case(s)

Start Processing Processing 100.00% There are 1 region(s) with p-value less than 1e-5. Please note that these results are inflated due to the overfitting inherent in finding the best-fit PRS (but it's still best to find the best-fit PRS!). You can use the --perm option (see manual) to calculate an empirical P-value.

Begin plotting Current Rscript version = 2.3.3 Plotting Bar Plot Plotting the high resolution plot (base) [redhaa@opti PRSice_linux]$ --perm 10000 bash: --perm: command not found... (base) [redhaa@opti PRSice_linux]$ #--pheno-col "ht_base","macrovascular_base","hist_macrovascular_base","macrovascular_tot","macrovascular_event","microvascular_base","hist_microvascular_base","microvascular_tot","microvascular_event","mi_base","mi_event","stroke_base","phenotype_tab","stroke_event","microalb_base","microalb_tot","microalb_event","macroalb_base","macroalb_tot","macroalb_event","micro_vascular_eye_disease","esrd","ht_hbp","current_smoking","cv_death","all_death","heart_fail_base","heart_fail_event","heart_fail_total","new_worse_retinopathy","double_crea","double_crea_5y","new_worse_neph" \ (base) [redhaa@opti PRSice_linux]$ #--pheno-col macrovascular_base (base) [redhaa@opti PRSice_linux]$ --thread 1 \

--binary-target T

bash: --thread: command not found... (base) [redhaa@opti PRSice_linux]$

[Sam]

1. You might want to reply in comment section instead of posting this as an answer. Otherwise, people might think this questions' been answered
2. Might want to format the log a bit better, but the problem is that you have a space behind \ possibly before the line of --pheno-col

[aredha2]

Thank you à lot Sam. I will come-back to you if I have any other question. Redha