something wrong installing with anaconda

[Haoyuan17]

Hello,

I use this to install with anaconda: conda config --add channels bioconda conda create -n vcf-kit python=2.7 vcfkit

And the error is:

UnsatisfiableError: The following specifications were found to be incompatible with each other Output in format: Requested package -> Available versions Package python conflicts for: vcfkit -> biopython -> python[version='3.4.|3.5.|3.6.|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0'] vcfkit -> python[version='2.7.|>=2.7,<2.8.0a0'] python=2.7

[Haoyuan17]

I find a biopython=1.69 version and then install vcfkit. Still not work. Error:

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications:

• vcfkit -> python[version='3.4.|3.5.|3.6.*|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0'] Your python: python=2.7 If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

[Haoyuan17]

I have solved the problem and it seems working well. The solution: conda create -n vcf-kit python=2.7 conda install matplotlib=2.2.5
conda install yahmm=1.1.2 pip install numpy==1.16.0 pip install VCF-kit

After this, find the "anaconda3/envs/vcf-kit/lib/python2.7/site-packages/vcfkit/utils/vcf.py" change line 11 "np.set_printoptions(threshold=np.nan)" to "np.set_printoptions(threshold=10000000000000)"

And it works. Because i cannot install vcfkit with conda(I don't know why.), I create a env of python2.7 with conda and then install the package which vcfkit need as the auther says. Maybe the numpy version or some other package version is different from the auther use, I have to change the code slightly. I believe it is a numpy version issue.

[danielecook]

@haoyuan17 I recommend installing vcf-kit in it's own environment.

I think you can simply do:

condo create -n vcf-kit vcf-kit

[Haoyuan17]

@danielecook At first I have used conda to install with the code： conda config --add channels bioconda conda create -n vcf-kit python=2.7 vcfkit

But there is a error as following:

[danielecook]

@Haoyuan17 what tools are you looking to use within vcf-kit? I am working on a new version that is compiled here: https://www.github.com/danielecook/seq-collection

Do you have docker installed? Python2 is being deprecated it looks like, so getting vcf-kit to work with Python3 will take some time.

One nice alternative you can try is running your analysis in a docker container.

docker pull ezequieljsosa/vcfkit

[Haoyuan17]

@danielecook Thanks a lot. My python version is 2.7 and I don't why I could not install vcf-kit easily. My friend could install in a few minutes, so it is the problem with my pc.

Actually I could use the vcf-kit now with a complicated process. I need the newick file and vcf-kit help me convert vcf to newick. The "vk phylo" command is good enough except for the large vcf file(I have a 50GB vcf file).

Do you have any advice on this issue: using "vk phylo" for large file?

I noticed that "seq-collection" could convert VCF to JSON. I am not familiar with JSON. Could I use JSON to get a newick file? How the JSON works with large file?

[Haoyuan17]

@danielecook I am writing to say the vcf-kit is really good. I mentioned about the large vcf file issue. It is not an issue. At first, I believe that I cannot run large file with my pc with a normal size RAM. I am wrong. The "vk phylo" command works well with the 50GB vcf.

When I use MEGA, online tools or other software, it is hard to get a fasta from vcf. I have to align the fasta and then make a phylo-tree. These takes a really long time more than vcf-kit. And my pc usually breakdown at the alignment step.

Thanks for your work and I would like to introduce the vcf-kit to my lab colleagues.

[danielecook]

Thanks!

[danielecook]

@Haoyuan17

I noticed that "seq-collection" could convert VCF to JSON. I am not familiar with JSON. Could I use JSON to get a newick file? How the JSON works with large file?

JSON format is not really useful from a genetics perspective; It is designed for sending data and might be useful if you wanted to send VCF data to a web browser.