OrthoMCL

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mysql configuration

changing tmp folder

Here is an example to move the mysqld tmpdir from /tmp to /run/mysqld which already exists on Ubuntu 13.04 and is a tmpfs (memory/ram):

sudo vim /etc/mysql/conf.d/local.cnf

Add:

[mysqld]

tmpdir = /run/mysqld

Then:

sudo service mysql restart

Last:

SHOW VARIABLES LIKE 'tmpdir';


If you get an error on MySQL restart, you may have AppArmor enabled:

sudo vim /etc/apparmor.d/local/usr.sbin.mysqld

Add:

  1. Site-specific additions and overrides for usr.sbin.mysqld.
  2. For more details, please see /etc/apparmor.d/local/README.

/run/mysqld/ r,

/run/mysqld/** rwk,

Then:

sudo service apparmor reload

만약에 이렇게 해도 안된다면 /etc/mysql/mysql.conf.d/mysqld.cnf 를 똑같은 방법으로 수정해보자

DBD::mysql::st execute failed: The total number of locks exceeds the lock table size at /alima9002/program/orthomclSoftware-v2.0.9/bin/orthomclPairs line 709, <F> line 15. Error

add or edit innodb_buffer_pool_size=10G on my.cnf or mysqld.cnf

All vs All blast command

blastp -db goodProteins.fasta -query goodProteins.fasta -outfmt 6 -out goodProteins.fasta.allvall -num_threads 3 -evalue 1e-5 -seg yes -soft_masking true -max_target_seqs 999999999