OrthoMCL problem when connecting with mysql

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5.8 years ago

Seq225 ▴ 110

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.

genome gene software error • 1.8k views

ADD COMMENT • link updated 5.6 years ago by Biostar 20 • written 5.8 years ago by Seq225 ▴ 110

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

ADD REPLY • link 5.8 years ago by Sishuo Wang ▴ 230

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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 REPLY • link 5.8 years ago by Carambakaracho ★ 3.2k

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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 REPLY • link 5.8 years ago by Seq225 ▴ 110

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