Longhao Jia

Hi, I also meet with the same problem.

You can just map reads to the contigs by minimap2 before calculating abundance by coverm. ##reference: https://github.com/deng-lab/viroprofiler/blob/main/modules/local/abundance.nf ##[WARNING] For a multi-part index, no @SQ lines will be outputted. Please use...

> I've looked into this a little more. > > First, my suggestion above was not 100% correct. That will get you python 3.7.0. To get the latest python 3.7...

I don't use Docker or other container service. Environment.yml file look like this: ``` name: DTR-phage-pipeline channels: - conda-forge - bioconda dependencies: - python == 3.7.* - snakemake >= 5.14.0...

> Hi, I tried to ran codes similar to vignette with my data, here are my code > > `df_age = res_prim_cagA %>% dplyr::select(taxon, ends_with("Age")) df_fig_age = df_age %>% dplyr::filter(diff_Age...

> Can vllm produce DNA sequence embedding? Since that the local pytorch inference for generating sequence embedding is too slow. Or there are some methods can produce fast sequence embedding...

> @callmest Can you provide a code snipet how you have tried to extract the embedding? If you want to get embedings, you can try the code in [issues 32](https://github.com/evo-design/evo/issues/32)。...

> I have fintune Evo with lora and then inference with cache on, i find that the inference with cache on was not right because i find that it's right...