Unable to install in new conda environment

[jeremysutherland]

Running: conda install vcf2gwas -c conda-forge -c bioconda -c fvogt257

I get an endless "spinning wheel" after "Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve."

Env details:

platform: linux-64
@explicit
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda
https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda
https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.2-hd590300_0.conda
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.42.0-h2797004_0.conda
https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2
**https://conda.anaconda.org/conda-forge/linux-64/python-3.9.17-h0755675_0_cpython.conda
https://conda.anaconda.org/conda-forge/noarch/setuptools-68.0.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/wheel-0.41.1-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/pip-23.2.1-pyhd8ed1ab_0.conda

[ttktjmt]

I encountered the same issue and found that utilizing mamba instead of conda was beneficial in pinpointing the environmental problem. You can install mamba with conda install mamba, and run mamba install vcf2gwas -c conda-forge -c bioconda -c fvogt257.

In my case, the problem was the lack of a specific python package, and the problem was solved by installing it.
I hope this works for you.

[nibrasissa]

Hi Tatsuki Tsujimoto,

I am getting an issue once I run the VCF2GWAS:

`(GWAStest) nibras@LAPTOP-0RVF794N:~/vcf2gwas-main$ vcf2gwas -v input/merged_file.vcf.gz -pf input/data.csv -ap -lmm

vcf2gwas v0.8.9

Initialising..

Start time: Wed, 08 Nov 2023 18:19

Parsing arguments..
Genotype file: merged_file.vcf.gz
Phenotype file(s): data.csv

Arguments parsed successfully

Preparing files

Checking data.csv..
Phenotype distribution(s) successfully plotted

Indexing VCF file..
VCF file already indexed
(GWAStest) nibras@LAPTOP-0RVF794N:~/vcf2gwas-main$
`

after trying to index, it states VCF file already indexed and not processed more

[ttktjmt]

Hi Nabras,

I am not familiar with this type of error, but this might be due to not having enough memory, especially when working with a large VCF file. If allocating enough memory is still not working, posting the problem as an issue could get you more specific advice.

Best

[Lattesnow]

have the same issue, try conda update --name base conda and conda update all