circle-map

安装circle-map

ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopyiki/Alphabet for more information.

查看一下安装的biopython版本

$python
>>> import Bio
>>> print(Bio.__version__)
1.81
quit（）

1.80的版本已经删掉了Alphabet 模块，先删掉当前版本的biopython，再安装1.76版本的biopython

pip3 unintall biopython
pip3 install biopython==1.76

再次运行已经安装成功

Circle-Map -h

1.下载测序数据，fastp clean data

2.准备参考基因组，解压

# hg38 reference文件
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/hg38.fa.gz
# hg38 md5sum文件，用于检查hg38 reference文件是否完整
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/md5sum.txt
md5sum hg38.fa.gz

##解压
tar -zxvf xxx.tar.gz
gunzip -d hg38.fa.gz

3.建立索引

bwa index hg38.fa

卡在sa

解决：切换到gpu-node