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.
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.
Comment