Difference between revisions of "OrthoMCL"

From Crop Genomics Lab.
Jump to: navigation, search
(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, line 15. Error)
 
(2 intermediate revisions by one user not shown)
Line 35: Line 35:
 
Then:
 
Then:
  
sudo service apparmor reload  
+
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===
 
===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
 
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

Latest revision as of 07:25, 6 February 2017

Contents

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 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