quast

quast 安装

conda crerate -n quast
conda activate quast
conda install -c bioconda quast

Preparing transaction: done
Verifying transaction: done
Executing transaction: | The default QUAST package does not include:
* GRIDSS (needed for structural variants detection)
* SILVA 16S rRNA database (needed for reference genome detection in metagenomic datasets)
* BUSCO tools and databases (needed for searching BUSCO genes) -- works in Linux only!

To be able to use those, please run
    quast-download-gridss
    quast-download-silva
    quast-download-busco

done
(quast)

quast-download-gridss
quast-download-silva
quast-download-busco
(quast)

gridss 和 silva 下载好了，busco出现了问题。看样子需要手动安装busco库。

augustus successfully downloaded!
  Done
  Downloading BUSCO database...
Downloading bacteria database (file: bacteria.tar.gz)...

ERROR! Failed downloading bacteria database (url: https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco/bacteria.tar.gz and restart QUAST
WARNING: Failed to download bacteria database from https://busco.ezlab.org/v2/datasets/bacteria_odb9.tar.gz and unpack it into /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco
  Downloading BUSCO database...
Downloading eukaryota database (file: eukaryota.tar.gz)...

ERROR! Failed downloading eukaryota database (url: https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco/eukaryota.tar.gz and restart QUAST
WARNING: Failed to download eukaryota database from https://busco.ezlab.org/v2/datasets/eukaryota_odb9.tar.gz and unpack it into /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco
  Downloading BUSCO database...
Downloading fungi database (file: fungi.tar.gz)...

ERROR! Failed downloading fungi database (url: https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz), QUAST functionality will be limited! Exception caught: HTTP Error 301: Moved Permanently
You can try to download the file manually, place it in /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco/fungi.tar.gz and restart QUAST
WARNING: Failed to download fungi database from https://busco.ezlab.org/v2/datasets/fungi_odb9.tar.gz and unpack it into /xtdisk/wangmx_group/ayunga/Software/miniconda/miniconda3/envs/quast/lib/python3.7/site-packages/quast_libs/busco
(quast)

去busco官网下载了最新的版本的库。放上述指定的位置。