bracken 运行错误

Question

bracken 运行错误

nohup bracken-build -d ~/db/kraken2-1 -t 8 -k 35 -l 150 &>bracken-build1.log &
运行报错
nohup: ignoring input
 >> Selected Options:
       kmer length = 35
       read length = 150
       database    = /gdata01/user/zhanggh/db/kraken2-1
       threads     = 8
       kraken type = kraken2
 >> Checking for Valid Options...
 >> Creating database.kraken [if not found]
          database.kraken exists, skipping creation....
          Finished creating database.kraken [in DB folder]
 >> Creating database150mers.kmer_distrib 
/gdata01/user/zhanggh/miniconda3/envs/zshmeta4/bin/bracken-build: line 194: kmer2read_distr: command not found

我去查该文件bracken-build: line 194

# check if kmer2read_distr is in PATH
elif [ -f $(command -v kmer2read_distr) ]; then
    kmer2read_distr --seqid2taxid $DATABASE/seqid2taxid.map --taxonomy $DATABASE/taxonomy/ --kraken $DATABASE/database.kraken --output $DATABASE/database${READ_LEN}mers.kraken -k ${KMER_LEN} -l ${READ_LEN} -t ${THREADS}
    if [ -f $(command -v generate_kmer_distribution.py) ]; then
        python $(command -v generate_kmer_distribution.py) -i $DATABASE/database${READ_LEN}mers.kraken -o $DATABASE/database${READ_LEN}mers.kmer_distrib
    else
        echo "      ERROR: generate_kmer_distribution.py script not found. "
        echo "          Run 'sh install_bracken.sh' to generate the kmer2read_distr script."
        echo "          Alternatively, cd to BRACKEN_FOLDER/src/ and run 'make'"
        exit
    fi
else
    echo "      ERROR: kmer2read_distr program not found. "
    echo "          Run 'sh install_bracken.sh' to generate the kmer2read_distr script."
    echo "          Alternatively, cd to BRACKEN_FOLDER/src/ and run 'make'"
    exit

应该怎么解决

Answer 1

参考GPT和自己的思路：

根据代码的提示信息，问题出现在第16行，原因是"kmer2read_distr"命令未找到。建议您按照以下步骤进行解决：

1. 检查kmer2read_distr是否存在于您的环境变量PATH中，您可以使用“echo $PATH”命令来检查。

2. 如果不存在于PATH中，可以将kmer2read_distr所在的文件夹路径添加到PATH中。

3. 如果kmer2read_distr不在任何路径中，请尝试重新安装bracken，因为bracken安装脚本中包含kmer2read_distr的生成步骤。

4. 如果以上解决方法都失败，请参考bracken安装文档或在bracken的GitHub页面上提交问题以获取更详细的帮助。