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:
- Site-specific additions and overrides for usr.sbin.mysqld.
- 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 line of my.cnf or mysqld.cnf
innodb_buffer_pool_size=10G
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