Question: OrthoMCL problem when connecting with mysql
0
gravatar for Seq225
21 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 • 748 views
ADD COMMENTlink modified 19 months ago by Biostar ♦♦ 20 • written 21 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 21 months ago • written 21 months ago by Sishuo Wang190

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 21 months ago by Carambakaracho2.0k

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 20 months ago by Seq22590
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