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Old 04-29-2014, 12:01 PM   #1
Junior Member
Location: the Netherlands

Join Date: Nov 2011
Posts: 6
Angry 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?

Last edited by melis; 04-29-2014 at 06:50 PM. Reason: problem changed
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