Question: OrthoMCL problem when connecting with mysql
0
gravatar for Seq225
10 months ago by
Seq22590
Seq22590 wrote:

Hi,

I am trying to use OrthoMCL. Having problem at the step 8. I am getting this message over and over again.

DBD::mysql::st execute failed: The used command is not allowed with this MySQL version at .......orthomclSoftware-v2.0.9/bin/orthomclLoadBlast line 39, <f> line 14.

My command was: ...bin/orthomclLoadBlast .....orthomclSoftware-v2.0.9/my_orthomcl_dir/orthomcl.config.template ....orthomclSoftware-v2.0.9/my_orthomcl_dir/compliantFasta/similarSequences

I have installed mysql-8.0.11-macos10.13-x86_64.dmg in MacOS High Sierra 10.13.6

I have tried to add: dbConnectString=dbi:mysql:orthomcl:mysql_local_infile=1 to my orthomcl.config.template file. Still not working.

Please help me. Thanks.

software error gene genome • 498 views
ADD COMMENTlink modified 8 months ago by Biostar ♦♦ 20 • written 10 months ago by Seq22590

You can try orthofinder or get_homologues instead for gene family clustering or identification of orthologs. Neither of them needs mysql connection.

ADD REPLYlink modified 10 months ago • written 10 months ago by Sishuo Wang170

you're working with a 2013 software (orthMCL) and a 2018 version of MySQL. In case you're not keen on reading the MySQL releas notes and then troubleshooting the orthoMCL source code to update all connection parameters, try an older release:

see https://en.wikipedia.org/wiki/MySQL#Release_history

ADD REPLYlink written 10 months ago by Carambakaracho1.1k

Thank you. Yes, that is the case. I tried older version of mysql. It was a mess (for me). Now I am trying to get the command for the new version.

ADD REPLYlink written 10 months ago by Seq22590
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