Closed scottdaniel closed 5 years ago
Hi @scottdaniel, You can find some suggestions about this issue here https://groups.google.com/d/msg/anvio/h-B_6w7kMco/gVk8o2lQBwAJ
Hiya,
It looks like doing this fixed it:
pip install https://github.com/scikit-learn/scikit-learn/archive/4035e60a6f0a0a2546bf0442ab603961c6a9cc4a.zip
In the anvio conda environment
After it installed the developer version of scikit-learn, I ran the mini-tests and the anvi-get-sequences-for-hmm-hits
:
anvi-get-sequences-for-hmm-hits --external-genomes external-genomes.txt \
> --list-hmm-sources
HMM SOURCES COMMON TO ALL 12 GENOMES
===============================================
* Rinke_et_al [type: singlecopy] [num genes: 1975]
* Campbell_et_al [type: singlecopy] [num genes: 1731]
* Ribosomal_RNAs [type: Ribosomal_RNAs] [num genes: 244]
* BUSCO_83_Protista [type: singlecopy] [num genes: 1741]
Another fix in #1202
Hi guys,
I'm on Mac OS Mojave 10.14.5 and have installed anvio using conda. I'm getting an error when running through the tutorial here http://merenlab.org/2017/06/07/phylogenomics/
Specifically, I get the error when using the command
anvi-get-sequences-for-hmm-hits
full output below...Here are the details of my conda anvio environment:
And
conda --version conda 4.7.5
Thanks Meren et al!