Question: DBI connect failed: orthomclLoadBlast
1
gravatar for max_19
25 days ago by
max_1950
max_1950 wrote:

Hi guys,

I am trying to run OrthoMCL on a remote server. When I get to the orthomclLoadBlast step, I keep getting this error message:

$ orthomclLoadBlast orthomcl.config similarSequences.txt

DBI connect('max_orthomcl','max',...) failed: Can't connect to local MySQL server through socket '/run/mysqld/mysqld.sock' (2)

I have been searching for a while, and it appears that the socket declaration should be in the my.cnf file. However socket is not specified in my.cnf file for me, and I cannot edit this file as part of the rules of using this server. Anyone know a way to fix this?

Not sure if this helps but here is the socket information if i do this in mysql:

$mysql
MariaDB [(none)]> show variables like 'socket';
+---------------+----------------------------+
| Variable_name | Value                      |
+---------------+----------------------------+
| socket        | /data/mariadb/mariadb.sock |
+---------------+----------------------------+
1 row in set (0.00 sec)

Any input is greatly appreciated.

orthomcl protein sequence mcl • 169 views
ADD COMMENTlink written 25 days ago by max_1950

are you sure you are using the correct credentials to access this remote SQL server? and set the ports to use correctly ?

ADD REPLYlink written 24 days ago by lieven.sterck4.5k

I made sure the credentials in the my.cnf file match those in the orthomcl.config (below)

dbVendor=mysql 
dbConnectString=dbi:mysql:max_orthomcl
dbLogin=max
dbPassword=Password
dbname=max_orthomcl
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-3
oracleIndexTblSpc=NONE

and I can see the database 'max_orthomcl' when I go into mysql

MariaDB [(none)]> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| max_orthomcl     |
+--------------------+

can you please let me know how i can check if ports are set up?

ADD REPLYlink written 24 days ago by max_1950
1

Are you running this on a compute cluster or such? If so , can you also check if you can actually access the MySQL server from the machine where you try to run OrthoMCL ?

ADD REPLYlink modified 24 days ago • written 24 days ago by lieven.sterck4.5k

Yes it is a compute cluster. I am trying to run both orthoMCL and MySQL from it. If I try to access mysql server using 'mysql' it appears to be working fine

$ mysql
Welcome to the MySQL monitor.  Commands end with ; or \g....etc etc

is there any other test I should try?

ADD REPLYlink modified 24 days ago • written 24 days ago by max_1950
1

yes, try to connect to the specific orthomcl DB from the cluster, something like following:

mysql -h <hostname> -u max  max_orthomcl -p

in other words, try to connect to the required DB from the commandline using the credentials from your config file

ADD REPLYlink modified 24 days ago • written 24 days ago by lieven.sterck4.5k

Thanks. I tried this and I got :

$ mysql -u max -D max_orthomcl -p password -h host
>Enter password: 
ERROR 1045 (28000): Access denied for user 'max' (using password: YES)
ADD REPLYlink modified 24 days ago • written 24 days ago by max_1950
2

voila there you have your answer: the 'max' account has no access to the mysql DB.

create an account on that server with the correct rights and then it should work. Alternatively try to use an account called orthomcl (it might be that that is the default one that is being created by orthomcl itself).

is your mysql server really called 'host' ?

ADD REPLYlink written 24 days ago by lieven.sterck4.5k
1

I will contact the cluster administrators then, thank you for the help! No that is not the actual host name (Just put that to show the command/arguments that were run).

ADD REPLYlink modified 24 days ago • written 24 days ago by max_1950

It's actually working now (I can access that specific DB from the cluster). apparently if you remove the space between -p and your password it works fine.

$ mysql -u max -D max_orthomcl -ppassword -h host

Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A

Welcome to the MariaDB monitor.  Commands end with ; or \g.
Server version: 10.2.13-MariaDB MariaDB Server

Copyright (c) 2000, 2016, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

MariaDB [max_orthomcl]>

any other ideas what could be causing the issue? I still get the same error when I try to run orthomclLoadBlast

ADD REPLYlink written 24 days ago by max_1950

Hmm, running out of ideas here.

perhaps this post can help you further: http://seqanswers.com/forums/archive/index.php/t-31112.html ? (start from the bottom)

ADD REPLYlink modified 23 days ago • written 23 days ago by lieven.sterck4.5k
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