Problem when installing orthomcl in step 4: orthomclInstallSchema

Question

[zengxi.hada]

I was installing the software orthomcl according to the user guide in http://www.orthomcl.org/common/downloads/software/v2.0/UserGuide.txt. When I processed to "Step 4: orthomclInstallSchema", I encountered problems.

$ orthomclInstallSchema orthomcl.config
OrthoMCLEngine::Main::Base=HASH(0xbffe98)
DBI connect('orthomcl:localhost:3307','orthomcl',...) failed: Access denied for user 'orthomcl'@'localhost' (using password: YES) at /home/zengxi/bin/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.

The content of orthomcl.config is

# this config assumes a mysql database named 'orthomcl'.  adjust according
# to your situation.
dbVendor=mysql
dbConnectString=dbi:mysql:orthomcl:localhost:3307
dbLogin=orthomcl
dbPassword=xxxx
similarSequencesTable=SimilarSequences
orthologTable=Ortholog
inParalogTable=InParalog
coOrthologTable=CoOrtholog
interTaxonMatchView=InterTaxonMatch
percentMatchCutoff=50
evalueExponentCutoff=-5
oracleIndexTblSpc=NONE

if I change dbConnectString=dbi:mysql:orthomcl:localhost:3307 to dbConnectString=dbi:mysql:orthomcl, the log information will be:

OrthoMCLEngine::Main::Base=HASH(0xefee98)
DBI connect('orthomcl','orthomcl',...) failed: Access denied for user 'orthomcl'@'localhost' (using password: YES) at /home/zengxi/bin/orthomclSoftware-v2.0.9/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 56.

Then I think that maybe if I change the user(dblogin) to root, it may work.

dbLogin=root
dbPassword=xxxx

However, it can't work either. The error log information is

$ orthomclInstallSchema orthomcl.config
OrthoMCLEngine::Main::Base=HASH(0x759e98)
OrthoMCLEngine::Main::Base=HASH(0x759e98)
DBD::mysql::st execute failed: Table 'InParalog' already exists at /home/zengxi/bin/orthomclSoftware-v2.0.9/bin/orthomclInstallSchema line 188, <F> line 14.

I tried so many times to fix it, but all failed. Did Anyone encounter this kind of problems before? I really appreciate it if you can help me to solve the problem.

Answer 1

[steven.kelly]

Hi, try OrthoFinder as an alternative. It's faster more accurate and much much easier to use

http://www.genomebiology.com/2015/16/1/157

[zengxi.hada]

Thank you. I will have a try.

[Eva_Maria]

its a very easy and accurate tool...thank uu