Error: Unrecognized flag ('--variant-score').
Peiyuan Zhu
> snpnet(ukb_imp_chr1_v3_trimmed_2m.bgen,ldl_pcs_joined_with_geno_path,"LDL")
[2021-02-12 11:43:02 snpnet] Start snpnet
[2021-02-12 11:43:02 snpnet] Preprocessing start..
Loading required namespace: glmnetPlus
Failed with error: ‘unable to load shared object '/home/zhupy/R/x86_64-pc-linux-gnu-library/4.0/glmnetPlus/libs/glmnetPlus.so':
libgfortran.so.4: cannot open shared object file: No such file or directory’
PLINK v2.00a2LM AVX2 Intel (25 Oct 2019) www.cog-genomics.org/plink/2.0/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to /tmp/RtmpKsopO5/meta/snpnet.train.log.
Options in effect:
--geno-counts cols=chrom,pos,ref,alt,homref,refalt,altxy,hapref,hapalt,missing,nobs
--keep /tmp/RtmpKsopO5/meta/snpnet.train.keep
--out /tmp/RtmpKsopO5/meta/snpnet.train
--pfile ukb_imp_chr1_v3_trimmed_2m vzs
--threads 1
Start time: Fri Feb 12 11:43:06 2021
257860 MiB RAM detected; reserving 128930 MiB for main workspace.
Allocated 7259 MiB successfully, after larger attempt(s) failed.
Using 1 compute thread.
92546 samples (48786 females, 43760 males; 92546 founders) loaded from
ukb_imp_chr1_v3_trimmed_2m.psam.
71109 variants loaded from ukb_imp_chr1_v3_trimmed_2m.pvar.zst.
1 quantitative phenotype loaded (92546 values).
--keep: 92546 samples remaining.
92546 samples (48786 females, 43760 males; 92546 founders) remaining after main
filters.
92546 quantitative phenotype values remaining after main filters.
Calculating allele frequencies... done.
--geno-counts: Genotype counts written to
/tmp/RtmpKsopO5/meta/snpnet.train.gcount .
End time: Fri Feb 12 11:43:08 2021
[2021-02-12 11:43:08 snpnet] Preprocessing end. Time elapsed: 6.1536 secs
[2021-02-12 11:43:08 snpnet] Iteration 0
[2021-02-12 11:43:08 snpnet] Start computeProduct()
[2021-02-12 11:43:08 snpnet] Start plink2 --variant-score
PLINK v2.00a2LM AVX2 Intel (25 Oct 2019) www.cog-genomics.org/plink/2.0/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to /tmp/RtmpKsopO5/results/residuals_iter_0.log.
Options in effect:
--keep /tmp/RtmpKsopO5/results/residuals_iter_0.tsv
--out /tmp/RtmpKsopO5/results/residuals_iter_0
--pfile ukb_imp_chr1_v3_trimmed_2m vzs
--read-freq /tmp/RtmpKsopO5/meta/snpnet.train.gcount
--threads 1
--variant-score /tmp/RtmpKsopO5/results/residuals_iter_0.tsv zs bin
Start time: Fri Feb 12 11:43:10 2021
Error: Unrecognized flag ('--variant-score').
For more info, try "plink2 --help <flag name>" or "plink2 --help | more".
zstd: can't stat /tmp/RtmpKsopO5/results/residuals_iter_0.vscore.vars.zst : No such file or directory -- ignored
Error in data.table::fread(paste0(fhead, ".cols"), head = F) :
File '/tmp/RtmpKsopO5/results/residuals_iter_0.vscore.cols' does not exist or is non-readable. getwd()=='/scratch/zhupy'
In addition: Warning messages:
1: In checkGlmnetPlus(out[["use.glmnetPlus"]], family) :
use.glmnetPlus was set to TRUE but glmnetPlus not found... Revert back to glmnet.
2: In data.table::fread(cmd = paste0(configs[["zstdcat.path"]], " ", :
File '/tmp/RtmpKsopO5/file7cce29119586' has size 0. Returning a NULL data.table.
(snpnet-deps-env) [zhupy@cedar5 zhupy]$ plink2 --help --variant-score
PLINK v2.00a2LM AVX2 Intel (25 Oct 2019) www.cog-genomics.org/plink/2.0/
(C) 2005-2019 Shaun Purcell, Christopher Chang GNU General Public License v3
No help entry for '--variant-score'.
