orthomcl error

[zxl124]

I ran into a problem running orthomcl for the first time. I was stuck at orthomclPairs step. Error message reads below.

DBD::mysql::st execute failed: Lost connection to MySQL server during query at ../bin/orthomclPairs line 693, <F> line 14.
Lost connection to MySQL server during query at ../bin/orthomclPairs line 693, <F> line 14.

The log file reads below:

Fri Jun 24 15:34:04 2011 configuration: dbVendor=mysql
Fri Jun 24 15:34:04 2011 configuration: dbConnectString=dbi:mysqlrthomcl:local
host:3307
Fri Jun 24 15:34:04 2011 configuration: dbLogin=orthomcl
Fri Jun 24 15:34:04 2011 configuration: dbPassword=********
Fri Jun 24 15:34:04 2011 configuration: similarSequencesTable=SimilarSequences
Fri Jun 24 15:34:04 2011 configuration: orthologTable=Ortholog
Fri Jun 24 15:34:04 2011 configuration: inParalogTable=InParalog
Fri Jun 24 15:34:04 2011 configuration: coOrthologTable=CoOrtholog
Fri Jun 24 15:34:04 2011 configuration: interTaxonMatchView=InterTaxonMatch
Fri Jun 24 15:34:04 2011 configuration: percentMatchCutoff=50
Fri Jun 24 15:34:04 2011 configuration: evalueExponentCutoff=-5
Fri Jun 24 15:34:04 2011 configuration: oracleIndexTblSpc=NONE
Fri Jun 24 15:34:04 2011 Constructing common temp tables
Fri Jun 24 15:34:04 2011 Find min evalue exp (OrthoMCL-DB V2 took ??? for thi
s step)
Fri Jun 24 15:34:05 2011 done
Fri Jun 24 15:34:05 2011 updating SimilarSequences, setting 0 evalue_exp to un
derflow value (-180 - 1) (Benchmark dataset took 25 min for this step)
Fri Jun 24 15:34:09 2011 step 'updateMinimumEvalueExponent' done (1 mins)

Fri Jun 24 15:34:09 2011 create BestQueryTaxonScore (Benchmark dataset took 1
.5 hours for this step)

It sounds like a problem with my mysql server, isn't it? But the previous steps were OK, and I am able to connect to it, so I am confused. Could anyone with experience with this program please help me fix this? Thank you very much.

[kmkocot]

I am having trouble at this step as well. The error I get is different, though.

orthomclPairs orthomcl.config orthomclPairs.log cleanup=yes
DBD::mysql::st execute failed: Table 'orthomcl.OrthologTemp' doesn't exist at /usr/local/orthomcl/bin/orthomclPairs line 668, <F> line 12.
Table 'orthomcl.OrthologTemp' doesn't exist at /usr/local/orthomcl/bin/orthomclPairs line 668, <F> line 12.

[rahularjun86]

Hi All,
I am also getting an error in the 4th Step "orthomclInstallSchema"

[rsharma@primary my_orthomcl_dir]$ orthomclInstallSchema orthomcl.config.template 
DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (22) at /home/rsharma/Software/orthomclSoftware-v2.0.3/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.
Can't connect to MySQL server on '3307' (22) at /home/rsharma/Software/orthomclSoftware-v2.0.3/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56, <F> line 14.

I did the mysql installations on my home directory without su privileges. I would really appreciate if someone could help me out.
Regards,
Rahul

[set]

Originally Posted by kmkocot

I am having trouble at this step as well. The error I get is different, though.

orthomclPairs orthomcl.config orthomclPairs.log cleanup=yes
DBD::mysql::st execute failed: Table 'orthomcl.OrthologTemp' doesn't exist at /usr/local/orthomcl/bin/orthomclPairs line 668, <F> line 12.
Table 'orthomcl.OrthologTemp' doesn't exist at /usr/local/orthomcl/bin/orthomclPairs line 668, <F> line 12.

Hi,

have you solved this? I get the same error but then already at the LoadBlast step.

Thank you

[kmkocot]

Unfortunately I didn't figure out my issue. I will probably work with this some more in the not too distant future so if I figure anything out I will let you know.

Kevin

[SES]

If you are unable to connect it could mean that the MySQL daemon isn't running. You should be able to do something like:

ps axu | grep mysqld

to check. Depending on how you configured MySQL, it may not be set to start automatically. This is a common reason for not being able to connect.

[klduong]

Originally Posted by rahularjun86

Hi All,
I am also getting an error in the 4th Step "orthomclInstallSchema"

[rsharma@primary my_orthomcl_dir]$ orthomclInstallSchema orthomcl.config.template 
DBI connect('orthomcl:3307','orthomcl',...) failed: Can't connect to MySQL server on '3307' (22) at /home/rsharma/Software/orthomclSoftware-v2.0.3/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.
Can't connect to MySQL server on '3307' (22) at /home/rsharma/Software/orthomclSoftware-v2.0.3/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56, <F> line 14.

I did the mysql installations on my home directory without su privileges. I would really appreciate if someone could help me out.
Regards,
Rahul

Even though this is an old post (and probably way too late for rahularjun86), I wanted to share my solution for other users (I spent too much time on this nonsense!).

Run netstat -tanp | grep mysqld
You should get something along the lines of:
tcp 0 0 0.0.0.0:#### 0.0.0.0:* LISTEN #####/mysqld

The #####/mysqld is the PID number--you don't care about this.
The number listed at 0.0.0.0:#### is the port number. This is what should be in orthomcl.config. For me it was set at 3306--the default port and what is assumed in orthomcl.config.template is 3307.

[akhilv]

I got same issue while running orthomcl load blast
"DBI connect('orthomcl:3307','root',...) failed: Can't connect to MySQL server on '3307' (22) at /home/eprints/clust/orthomclSoftware/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.''

how to solve this?