alphafold Could find neither hhm_db nor a3m_db 解决日志
报错日志 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in <module> app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 429, in main is_prokaryote=is_prokaryote) File "/app/alphafold/run_alphafold.py", line 177, in predict_structure msa_output_dir=msa_output_dir) File "/app/alphafold/alphafold/data/pipeline.py", line 225, in process use_precomputed_msas=self.use_precomputed_msas) File "/app/alphafold/alphafold/data/pipeline.py", line 101, in run_msa_tool result = msa_runner.query(input_fasta_path)[0] File "/app/alphafold/alphafold/data/tools/hhblits.py", line 144, in query stdout.decode('utf-8'), stderr[:500_000].decode('utf-8'))) RuntimeError: HHblits failed stdout: stderr: - 02:15:01.531 ERROR: Could find neither hhm_db nor a3m_db! 资料收集RuntimeError: HHblits failed #9 重新下载所有数据文件HHblits failed #12 虚拟内存不足 扩展虚拟内存后无改善HHblits failed #14 重新下载bfd数据文件Singularity - HHblits: Could find neither hhm_db nor a3m_db #202 运行权限问题`HHblits failed: no stdout and no stderr message #211 CPU avx2指令集 兼容性RuntimeError: HHblits failed #284 物理内存不足32G/reduced_dbs问题排查更改运行指令增加：--db_preset=reduced_dbs, 使用快速预测模式，正常单步执行Dockerfile指令，自己构建一个镜像实例从Dockfile中提取关键镜像为:nvidia/cuda:11.1-cudnn8-runtime-ubuntu18.04，基于这个镜像创建docker实例并进入sudo docker run -it --name alphafold-ldmf -v /pathTo/alphafold/:/data/alphafold -v /pathTo/alphafold-data/:/data/alphafold-data --runtime=nvidia -e NVIDIA_VISIBLE_DEVICE=all nvidia/cuda:11.1-cudnn8-runtime-ubuntu18.04修改dns和pip源，并单步执行Dockerfile下的每一行操作/etc/resolv.confnameserver 114.114.114.114 nameserver 8.8.8.8 nameserver 119.29.29.29 nameserver 223.5.5.5 git克隆alphafold_non_docker项目wget下载alphafold-v2.1.1release代码(alphafold_non_docker作者还没支持最新的v2.1.2),并解压放到alphafold_non_docker下修改alphafold_non_docker下的run_alphafold.sh,将alphafold的路径配置好 current_working_dir=$(pwd) 改为 current_working_dir=$(pwd)/alphafold-2.1.1复制测试T1050.fasta文件，运行bash run_alphafold.sh -d /data/alphafold-data -o /data/alphafold-result -f /data/alphafold/T1050.fasta -t 2020-05-14 报错RT基于日志，得到单步指令，运行HHblits/usr/bin/hhblits -i /data/alphafold/T1050.fasta -cpu 4 -oa3m /tmp/tmpsv9qnin5/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data/alphafold-data/origin_bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data/alphafold-data/uniclust30/uniclust30_2018_08/uniclust30_2018_08搜索hhblits，得到git仓库地址，克隆之后，根据源码，确认第8步命令实际是读取：/data/alphafold-data/origin_bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt下的.ffindex和.ffdata文件/data/alphafold-data/uniclust30/uniclust30_2018_08/uniclust30_2018_08下的.ffindex和.ffdata文件观察到这两个目录下有.ffindex和.ffdata,但没有r权限，所以，chmod给读取权限重新运行，等待，等待，等待，问题解决。解决方式确认并将alphafold数据文件的权限，并给所有的文件加读权限cd /pathTo/alphafold-data/chmod -R +r ./*即：资料收集的Singularity - HHblits: Could find neither hhm_db nor a3m_db #202验证有效，需要将数据文件改权限。附录alphafoldalphafold_non_dockerhh-suite
解决AlphaFold的官方Dockerfile构建时报错 Temporary failure resolving 'developer.download.nvidia.cn'
问题RT，在构建alphaFold的时候:docker build -f docker/Dockerfile -t alphafold .执行构建docker的时候报错，分析构建过程：在apt-get update命令处提示:Err:13 https://developer.download.nvidia.cn/compute/cuda/repos/ubuntu1804/x86_64 InRelease Temporary failure resolving 'developer.download.nvidia.cn' Err:14 https://developer.download.nvidia.cn/compute/machine-learning/repos/ubuntu1804/x86_64 InRelease Temporary failure resolving 'developer.download.nvidia.cn'并且紧接着造成连锁错误：W: Failed to fetch https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/InRelease Temporary failure resolving 'developer.download.nvidia.cn' W: Failed to fetch https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64/InRelease Temporary failure resolving 'developer.download.nvidia.cn' W: Some index files failed to download. They have been ignored, or old ones used instead. 解决方案 - 修改DNS修改docker的守护参数sudo nano /etc/docker/daemon.json追加dns相关配置"dns":["114.114.114.114","8.8.8.8","119.29.29.29","223.5.5.5"]sudo systemctl daemon-reload sudo systemctl restart docker然后重新运行构建命令docker build -f docker/Dockerfile -t alphafold .问题解决。附录docker部署ubuntu18.04深度学习环境Unable to locate package cuda-command-line-tools在Ubuntu中设置DNS域名服务器(转）修改容器的 DNS 服务器