<p>Try the latest plink 2.0 alpha build for this.  It’s an incomplete program, but its implementation of —linear is far better than v1.9’s.</p>

CC BY-SA 4.0
2019-01-21T09:59:08.613Z
Thank you! I have a little issue with the covariate-related. I have asked on Biostars here: https://www.biostars.org/p/359523/. Could you please have a look? Thank you!
user2842390
CC BY-SA 4.0
2019-01-21T06:34:30.040Z
2019-01-21T06:34:30.040Z
Christopher Chang
<p>I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used <code>--threads &lt;num of cores&gt;</code> but it says it only uses 1 thread</p>

<p>here is my code for the calculation in plink:</p>

<pre><code>plink --bfile ukbb_dis --pheno phenotype_dis.pheno --mpheno 4 --allow-no-sex --covar phenotype_dis.pheno --covar-number 5-21 --missing-phenotype -10000000 --linear --adjust --out assoc_SNP_height_linear --threads 4
</code></pre>

<p>Here is the current output:</p>

<pre><code>257682 MB RAM detected; reserving 128841 MB for main workspace.
1133273 variants loaded from .bim file.
284516 people (0 males, 0 females, 284516 ambiguous) loaded from .fam.
Ambiguous sex IDs written to assoc_SNP_height_linear.nosex .
284516 phenotype values present after --pheno.
Using 1 thread.
Warning: This run includes BLAS/LAPACK linear algebra operations which
currently disregard the --threads limit.  If this is problematic, you may want
to recompile against single-threaded BLAS/LAPACK.
--covar: 17 out of 21 covariates loaded.
Before main variant filters, 284516 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.992737.
1133273 variants and 284516 people pass filters and QC.
Phenotype data is quantitative.
Writing linear model association results to
assoc_SNP_height_linear.assoc.linear ... 0%
</code></pre>

<p>Your help is really appreciated!</p>

<gwas><plink>
Parallel in PLINK for linear association for SNP effects
# Parallel in PLINK for linear association for SNP effects

(Asked by: username_0 on 2019-01-21)

I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used --threads  but it says it only uses 1 thread
here is my code for the calculation in plink:
plink --bfile ukbb_dis --pheno phenotype_dis.pheno --mpheno 4 --allow-no-sex --covar phenotype_dis.pheno --covar-number 5-21 --missing-phenotype -10000000 --linear --adjust --out assoc_SNP_height_linear --threads 4

Here is the current output:
257682 MB RAM detected; reserving 128841 MB for main workspace.
1133273 variants loaded from .bim file.
284516 people (0 males, 0 females, 284516 ambiguous) loaded from .fam.
Ambiguous sex IDs written to assoc_SNP_height_linear.nosex .
284516 phenotype values present after --pheno.
Using 1 thread.
Warning: This run includes BLAS/LAPACK linear algebra operations which
currently disregard the --threads limit.  If this is problematic, you may want
to recompile against single-threaded BLAS/LAPACK.
--covar: 17 out of 21 covariates loaded.
Before main variant filters, 284516 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.992737.
1133273 variants and 284516 people pass filters and QC.
Phenotype data is quantitative.
Writing linear model association results to
assoc_SNP_height_linear.assoc.linear ... 0%

Your help is really appreciated!

**Tags:** gwas, plink

---

## 1 answers

### Answer by username_1 on 2019-01-21. Score: 2 | Accepted answer

Try the latest plink 2.0 alpha build for this. It’s an incomplete program, but its implementation of —linear is far better than v1.9’s.

> **Comments:**
> **username_0**: Thank you! I have a little issue with the covariate-related. I have asked on Biostars here: https://www.biostars.org/p/359523/. Could you please have a look? Thank you!  

---

