Open jeremysutherland opened 1 year ago
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.
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
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
have the same issue, try conda update --name base conda and conda update all
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