`Too many phenotype input files for available ressources` [sic]

[hhg7]

I'm running a test of my recent installation:

(myenv) con@V:~/Downloads/tmp$ vcf2gwas -v test

vcf2gwas v0.6.1 

Initialising..

Copying example input files to current working directory..
Copying README and LICENSE files..
Start time: Mon, 19 Jul 2021 14:53:50

Parsing arguments..
Genotype file: example.vcf.gz
Phenotype file(s): example.csv
Arguments parsed successfully

Preparing files
Error: Too many phenotype input files for available ressources

this is being done in an empty directory, I don't know where there can be any input files.

[frankvogt]

This is caused by vcf2gwas using the internal test files and it seems that there is not enough memory available to analyze the test phenotype (1 GB is the minimal requirement). Try to set the memory manually to at least 1000 (MB) with the -M / --memory option. To check the resources available to vcf2gwas you can type "vcf2gwas -h" and check the values displayed at the "-M" and "-T" options

[frankvogt]

Also, please update to the newest version by running "conda update vcf2gwas -c conda-forge -c bioconda -c fvogt257"

[hhg7]

Hi Frank,

thanks. I've re-installed and updated conda as you said, but am now running into new errors:

(vcf2gwas) con@V:~/Downloads$ vcf2gwas -v test -T 9

vcf2gwas v0.6.2 

Initialising..

Copying example input files to current working directory..
Copying README and LICENSE files..
Start time: Wed, 21 Jul 2021 09:32:08

Parsing arguments..
Genotype file: example.vcf.gz
Phenotype file(s): example.csv
Arguments parsed successfully

Preparing files

Error: No logical cores available!

setting the # of cores with -T doesn't seem to work :(

[frankvogt]

Can you check with "vcf2gwas -h" under the -T option which number of cores is displayed in brackets?

[frankvogt]

Can the issue be closed?

[hhg7]

Yes please close the issue

On Fri, Sep 3, 2021, 17:23 Frank Vogt @.***> wrote:

Can the issue be closed?

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