Error: Cannot open file: 510

[theclairecamp]

Issue I have used the recommended input files but am getting an error. This is the exact line of code I used to run PRSice: Rscript PRSice.R --dir . --prsice PRSice_mac --base Base_Data.gz --target Target_Final --binary-target F --pheno Final.phenotype --cov Final.covariate --ignore-fid --clump-r2 0.25 --clump-kb 200 --fastscore T --x-range chr6:28,510,120-33,480,577 --stat OR

I am running the code in the directory with all the files necessary. The phenotype and covariates are tab-delimited files, and the Target_Final.bed/bim/fam files are located within the current directory. I'm wondering what exactly isn't loading, I tried looking at the specific line of code in PRSice.R to figure it out but still haven't figured out the bug yet. I'm thinking maybe it's a simple issue with formatting somewhere?

Error Log This is the error log that popped up:

Error: Cannot open file: 510 

Begin plotting
Current Rscript version = 2.3.3
Error in fread(paste0(argv$out, ".summary"), data.table = F) : 
  File 'PRSice.summary' does not exist or is non-readable. getwd()=='/Users/claire/Desktop/Genotype/PRSice_mac'
Execution halted

To Reproduce Here is the PRSice log file info: PRSice 2.3.5 (2021-09-20) 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) 2022-05-16 15:29:02 ./PRSice_mac
--a1 A1
--a2 A2
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--base Base_Data.gz
--base-info INFO:0.9
--binary-target F
--bp BP
--chr CHR
--clump-kb 200kb
--clump-p 1.000000
--clump-r2 0.250000
--cov Final.covariate
--fastscore
--ignore-fid
--num-auto 22
--or
--out PRSice
--pheno Final.phenotype
--pvalue P
--seed 1941739298
--snp SNP
--stat OR
--target Target_Final
--thread 1
--x-range chr6:28,510,120-33,480,577

Error: Cannot open file: 510

Thanks for you help!

[choishingwan]

Hi, that's because your x-range command contains comma which was interpreted as a file input instead of range (see that the missing file name is 510). Remove the comma from the range input and you should be good to go

On Mon, May 16, 2022, 6:47 PM Claire Campbell @.***> wrote:

Bug I have used the recommended input files but am getting an error. This is the exact line of code I used to run PRSice: Rscript PRSice.R --dir . --prsice PRSice_mac --base Base_Data.gz --target Target_Final --binary-target F --pheno Final.phenotype --cov Final.covariate --ignore-fid --clump-r2 0.25 --clump-kb 200 --fastscore T --x-range chr6:28,510,120-33,480,577 --stat OR

I am running the code in the directory with all the files necessary. The phenotype and covariates are tab-delimited files, and the Target_Final.bed/bim/fam files are located within the current directory. I'm wondering what exactly isn't loading, I tried looking at the specific line of code in PRSice.R to figure it out but still haven't figured out the bug yet. I'm thinking maybe it's a simple issue with formatting somewhere?

Error Log This is the error log that popped up:

Error: Cannot open file: 510

Begin plotting Current Rscript version = 2.3.3 Error in fread(paste0(argv$out, ".summary"), data.table = F) : File 'PRSice.summary' does not exist or is non-readable. getwd()=='/Users/claire/Desktop/Genotype/PRSice_mac' Execution halted

To Reproduce Here is the PRSice log file info: PRSice 2.3.5 (2021-09-20) 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) 2022-05-16 15:29:02 ./PRSice_mac --a1 A1 --a2 A2 --bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1 --base Base_Data.gz --base-info INFO:0.9 --binary-target F --bp BP --chr CHR --clump-kb 200kb --clump-p 1.000000 --clump-r2 0.250000 --cov Final.covariate --fastscore --ignore-fid --num-auto 22 --or --out PRSice --pheno Final.phenotype --pvalue P --seed 1941739298 --snp SNP --stat OR --target Target_Final --thread 1 --x-range chr6:28,510,120-33,480,577

Error: Cannot open file: 510

Thanks for you help!

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/295, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYXHGTZTZDDZNWWNID3VKLGB3ANCNFSM5WC7SELQ . You are receiving this because you were assigned.Message ID: @.***>

[theclairecamp]

THANK YOU! That was it! I was wondering where 510 was coming from...I really appreciate your response. (also, I've tried to remove the 'bug' label but I can't seem to remove it...my bad)