Is it possible to run vcf2gwas multiple times simultaneously?

[vinod1981]

Dear Frank, Not a question directly related to vcf2gwas but rather looks a question with conda but may be you have an answer.

Can I run vcf2gwas simultaneously multiple time by submitting the job arrays (2 or more) for different traits? Actually, when I do it, one of the job is aborted so for now I have to wait until my first job is completed?

Even I can't run two jobs by activating the conda env once in the job arrays. Is their any hack to get over these limitations?

Thanks,

Vinod

[frankvogt]

Hi Vinod, If you want to analyze different traits (on the same gentoype data set) just put them in the same phenotype file as described in the manual and run the analysis on all phenotypes. The analyses of the phenotypes will be done in parallel by vcf2gwas.

Otherwise you can try to run vcf2gwas in two different conda environments but as of right now you would also need to run each instance in a separate directory as the two runs would interfere with each other (I will fix that in a future version).

Hope that helps! Frank

[vinod1981]

Dear Frank,

Thanks for the reply. Actually, the datasets are different and I am using different parameters for them so, can't put them in same file. That is what happening when I am trying them from different env they are interfering with each other, probably because they are using the same temp space. It would be great if we can run them separately as sometime we need to wait until the previous run in completed. Thanks, Vinod,

[frankvogt]

Hi Vinod, I see. Indeed in the current version they use the same temp space if you run the analyses from the same directory. I will fix that in the next version. For now you could just run each analysis from a different directory for a quick fix. Best, Frank

[frankvogt]

From version v0.8.8 onwards you can run vcf2gwas simultaneously multiple times from the same directory.