Open HaimAshk opened 1 year ago
Having the same issue. I post this to follow the thread.
I have similar issues as well.
I have a similar issue too. Wondering who has solved this issue?
Hi all,
It looks like an update on python is breaking the code. It takes sometime to get the conda installation updated. Meanwhile, you use ANY of the solutions below:
1) use option 3 (the apptainer image). @Guillaume-Marseille, the image has database and dependencies included within it, so it's the most stable and reliable. You can run it directly w/o database setup, eg. /path/to/virsorter2.sif run -w test.out -i test.fa --min-length 1500 -j 4 all
2) With a new conda install, use this mamba create -n vs2 -c conda-forge -c bioconda virsorter=2 conda-package-handling=1.9
3) With the conda version that you are getting this error, run the this command line before running VS2: export PYTHONWARNINGS="ignore::Warning"
Hi, I used the following commands:
mamba create -c bioconda -c conda-forge -p /path/to/conda_envs/ViWrap-vs2 python=3.8 virsorter=2.2.4 numpy=1.20.0 -y
export PYTHONWARNINGS="ignore::Warning"
virsorter setup -d VirSorter2_db -j 4
But I still failed to use virsorter2 and download the database:
@ChaoLab , how did you activate the ViWrap-vs2
env (something like conda activate ViWrap-vs2
) before the export
command?
The following works in my test:
mamba create -c conda-forge -c bioconda -n vs2 python=3.8 virsorter=2.2.4 -y
conda activate vs2
export PYTHONWARNINGS="ignore::Warning"
virsorter setup -d VirSorter2_db -j 4
@jiarong Yes, I was in the conda env
@ChaoLab , how did you activate the ViWrap-vs2 env? I am wondering the way getting in the env might make a difference..
It is “conda activate /storage2/scratch/zzhou388/ViWrap/conda_envs/ViWrap-vs2”
@ChaoLab , no clue why it works in my server but not yours.. For conda version, you can also try the following:
mamba create -n vs2 -c conda-forge -c bioconda virsorter=2 conda-package-handling=1.9
Dear @jiarong,
Thanks for your help! The third option export PYTHONWARNINGS="ignore::Warning"
solved the problem for me 😄
@jiarong
I tried:
mamba create -p /storage2/scratch/zzhou388/ViWrap/conda_envs/ViWrap-vs2 -c conda-forge -c bioconda virsorter=2.2.4 conda-package-handling=1.9 numpy=1.20.0 -y
and then get into the conda env by:
conda activate /storage2/scratch/zzhou388/ViWrap/conda_envs/ViWrap-vs2
and then want to download the db by:
virsorter setup -d VirSorter2_db -j 20
But it failed in the same way:
Hi,
Thanks for maintaining this tool. I have installed the latest Virsorter2 development version (from github) into a new conda env, following the instructions in 'option 2'
When trying to run it with the example sequence provided I get the following error:
virsorter run -w test.out -i test.fa --min-length 1500 -j 4 all
This is ow my conda env looks like: conda list
Same happened when installing using the instructions under 'option 1'. Any advice how to solve it?
Thanks in advance for any suggestion!