Orthomcl Pairs error

melis · 04-29-2014, 12:01 PM

Hello everyone,

I am trying to get orthomcl running for my non-model organism and I am using cDNA sequences for 6 species in total. I created a blastdb index with the goodproteins.fasta created in Filterfasta step and ran a blastall against that with the same goodproteins.fasta file. I came up to Pairs step with no problem. But orthomclPairs did not finish and gave a duplicate entry error at 'best_hit_ix' step:

"DBD::mysql::st execute failed: Duplicate entry 'Ath|AT1G01020.1-Pre|comp61821_c1_seq31' for key 'best_hit_ix' at /share/apps/orthomcl-2.0.9/bin/orthomclPairs line 709, <F> line 16."

I checked the gene ID in the error, but there seems to be no replicate apart from the reciprocal hits (since the db index and the query are the same files).

I read on a forum that restarting the whole procedure eliminated this error, so I started it again from step1. However that did not help either.

Do you have any suggestions to avoid this error and continue the procedure?
Thanks!

fireLog2 · 06-10-2014, 09:19 AM

This error can occur if you didn't remove the old entries in your mysql database. If you re-add your similarSequences.txt in the same database, the entries will be double.

I'm not sure if the command ./bin/orthomclDropSchema orthomcl.config sql_dropTable.log does this job.
I log in mysql and use 'DROP DATABASE orthomcl;' Then re-create the database and load the similarSequences file.

If this error also occurs after the first time. Then you messed around with your blast or similarSequences file and have double entries.

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04-29-2014, 12:01 PM	#1
melis Junior Member Location: the Netherlands Join Date: Nov 2011 Posts: 6	Orthomcl Pairs error Hello everyone, I am trying to get orthomcl running for my non-model organism and I am using cDNA sequences for 6 species in total. I created a blastdb index with the goodproteins.fasta created in Filterfasta step and ran a blastall against that with the same goodproteins.fasta file. I came up to Pairs step with no problem. But orthomclPairs did not finish and gave a duplicate entry error at 'best_hit_ix' step: "DBD::mysql::st execute failed: Duplicate entry 'Ath\|AT1G01020.1-Pre\|comp61821_c1_seq31' for key 'best_hit_ix' at /share/apps/orthomcl-2.0.9/bin/orthomclPairs line 709, <F> line 16." I checked the gene ID in the error, but there seems to be no replicate apart from the reciprocal hits (since the db index and the query are the same files). I read on a forum that restarting the whole procedure eliminated this error, so I started it again from step1. However that did not help either. Do you have any suggestions to avoid this error and continue the procedure? Thanks! Last edited by melis; 04-29-2014 at 06:50 PM. Reason: problem changed

06-10-2014, 09:19 AM	#2
fireLog2 Member Location: Germany Join Date: Jul 2013 Posts: 10	This error can occur if you didn't remove the old entries in your mysql database. If you re-add your similarSequences.txt in the same database, the entries will be double. I'm not sure if the command ./bin/orthomclDropSchema orthomcl.config sql_dropTable.log does this job. I log in mysql and use 'DROP DATABASE orthomcl;' Then re-create the database and load the similarSequences file. If this error also occurs after the first time. Then you messed around with your blast or similarSequences file and have double entries.