mysql和ORTHOMCL_orthomcl安装和配置

安装：

conda install orthomcl

复制orthomcl.config.template到工作目录下，改名为orthomcl.config

修改orthomcl.config的内容如下：

# this config assumes a mysql database named 'orthomcl'. adjust according

# to your situation.

dbVendor=mysql

dbConnectString=dbi:mysql:orthomcl:mysql_local_infile=1

dbLogin=Your_username

dbPassword=Your_password

similarSequencesTable=SimilarSequences

orthologTable=Ortholog

inParalogTable=InParalog

coOrthologTable=CoOrtholog

interTaxonMatchView=InterTaxonMatch

percentMatchCutoff=50

evalueExponentCutoff=-5

oracleIndexTblSpc=NONE

创建账户并运行

为了避免其它问题，用root账户登入mysql并把下面的命令运行一遍就行了。

mysql -uroot -ppasswd

CREATE USER 'jiayuxin'@'localhost' IDENTIFIED BY '111111'; #创建账户

grant all privileges on orthomcl.* to 'jiayuxin'@'localhost'; #把database orthomcl的权限授权给账户

ALTER USER 'jiayuxin'@'localhost' IDENTIFIED WITH mysql_native_password BY '111111'; #更改加密方法

也可以直接用自己的账户创建一个database，就不用root用户给授权了，以下是常用命令。

mysql -ujiayuxin -p111111

drop database orthomcl; #删除名为orthomcl的database

create database orthomcl; #创建一个名为orthomcl的database

show databases; #查看账户下存在的databases

使用root账户登录mysql

mysql -u root -p

输入密码进去mysql，使用SHOW VARIABLES LIKE 'local_infile';查看当前local_infile状态为OFF。

mysql> SHOW VARIABLES LIKE 'local_infile';

+---------------+-------+

| Variable_name | Value |

+---------------+-------+

| local_infile | OFF |

+---------------+-------+

1 row in set (0.00 sec)

使用SET GLOBAL local_infile = 1;修改local_infile格式，重新用SHOW VARIABLES LIKE 'local_infile';查看：

mysql> SHOW VARIABLES LIKE 'local_infile';

+---------------+-------+

| Variable_name | Value |

+---------------+-------+

| local_infile | ON |

+---------------+-------+

1 row in set (0.01 sec)

可以了。

运行到orthomclPairs时，出现错误提示DBD::mysql::st execute failed: The total number of locks exceeds the lock table size，查到两种办法，一种修改tmp变量的大小，另一种修改innodb_buffer_pool_size，都试一下。

进入mysql，输入show variables like "%tmp%";查看tmp大小：

mysql> show variables like "%tmp%";

+---------------------------------+-----------+

| Variable_name | Value |

+---------------------------------+-----------+

| default_tmp_storage_engine | InnoDB |

| innodb_tmpdir | |

| internal_tmp_mem_storage_engine | TempTable |

| slave_load_tmpdir | /tmp |

| tmp_table_size | 16777216 |

| tmpdir | /tmp |

+---------------------------------+-----------+

6 rows in set (0.02 sec)

修改为1G：

SET GLOBAL tmp_table_size =1024*1024*1024;

改完之后好像没变化，先不管，接着查看innodb_buffer_pool_size：

mysql> show variables like "%_buffer%";

+-------------------------------------+----------------+

| Variable_name | Value |

+-------------------------------------+----------------+

| bulk_insert_buffer_size | 8388608 |

| innodb_buffer_pool_chunk_size | 134217728 |

| innodb_buffer_pool_dump_at_shutdown | ON |

| innodb_buffer_pool_dump_now | OFF |

| innodb_buffer_pool_dump_pct | 25 |

| innodb_buffer_pool_filename | ib_buffer_pool |

| innodb_buffer_pool_in_core_file | ON |

| innodb_buffer_pool_instances | 1 |

| innodb_buffer_pool_load_abort | OFF |

| innodb_buffer_pool_load_at_startup | ON |

| innodb_buffer_pool_load_now | OFF |

| innodb_buffer_pool_size | 134217728 |

| innodb_change_buffer_max_size | 25 |

| innodb_change_buffering | all |

| innodb_log_buffer_size | 16777216 |

| innodb_sort_buffer_size | 1048576 |

| join_buffer_size | 262144 |

| key_buffer_size | 8388608 |

| myisam_sort_buffer_size | 8388608 |

| net_buffer_length | 16384 |

| preload_buffer_size | 32768 |

| read_buffer_size | 131072 |

| read_rnd_buffer_size | 262144 |

| sort_buffer_size | 262144 |

| sql_buffer_result | OFF |

+-------------------------------------+----------------+

25 rows in set (0.00 sec)

改为3G：

mysql> SET GLOBAL innodb_buffer_pool_size=3*1024*1024*1024;

Query OK, 0 rows affected (0.00 sec)

重新运行试试。

提示错误DBD::mysql::st execute failed: The table 'InplgOrthoInplg' is full at /Some_path/，查了下原因可能有两种：1.存放mysql数据的硬盘满了。2.参数设置太小了。

第一种情况，尝试更改mysql数据存放位置，始终报错，暂时放在原处，还够用。

第二种情况，在/etc/my.cnf文件中[mysqld]字段下面添加命令innodb_data_file_path=ibdata1:10G:autoextend，重新运行试试。