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  • OrthoMCL duplicate entry error

    I have made it up to step 10 of the orthomcl process, finding protein pairs, but have become stuck with a duplicate entry error:

    Duplicate entry '5206|CNAG_00003-5206|CNE00390' for key 'better_hit_ix' at /data/ngs/apps/orthomclSoftware/bin/orthomclPairs line 693, <F> line 14

    I thought maybe it was something to do with the way I ran BLAST so I reran with parameters recommended but still get an error, although a different one:

    Duplicate entry '5206|CNAG_00006-5206--181-0-5206-5206|CNAG_00006' for key 'ss_qtaxexp_ix' at /data/ngs/apps/orthomclSoftware/bin/orthomclPairs line 693, <F> line 14

    Has anyone had a similar issue?

    Thanks for your help

  • #2
    the duplicate entry error can be removed by selecting only the distinct rows in the similarSequence table

    Comment


    • #3
      Originally posted by jollymrt View Post
      the duplicate entry error can be removed by selecting only the distinct rows in the similarSequence table
      Never mind. There was a duplicate or two that I had missed. Sorting and using the tool 'uniq' works but you have to use the command -w and a number (I used 40) to limit the match to just the accession - sometimes the duplicates had different score values and so were effectively unique... Phew.

      Any chance you could expand on that?

      I have the same error as the OP, my file is 6.5GB.

      I've gone through the file and removed duplicates...or at least I thought I had.

      I managed to find a list of duplicate accessions and so removed them from similarsequences with AWK. I then also sorted the file on the first column and performed a uniq removal of any next neighbour duplicates...

      Every time the same error:
      Duplicate entry 'didi|DDB_G0279353-didi|DDB_G0283451' for key 'better_hit_ix' at /home/cs02gl/programs/orthomclSoftware-v2.0.3/bin/orthomclPairs line 693, <F> line 14.

      Looking at those accessions in the file (using grep) reveals no duplicates for that matching.
      Last edited by guyleonard; 01-07-2013, 03:39 AM.

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      • #4
        to check if you have duplicate entries use the following command

        select * from similarSequences group by query_id,subject_id having count(*)>1;

        this command will give you the rows that are duplicated.

        Then you can create a new table that will have only distinct rows.

        create table holdup as select distinct * from similarSequences;

        Comment


        • #5
          I am also having the same errors as the OP.

          Apart from trying ways to fix it I am wondering what causes the duplicate error in the orthoMCL pipeline. Given that duplicates are to be expected after an all-vs-all blast I would expect that the orthoMCL scripts would appropriately deal with them.

          Is this a matter of orthomclBlastParser, orthomclLoadBlast or orthomclPairs not doing a proper job?

          Originally posted by jollymrt View Post
          to check if you have duplicate entries use the following command

          select * from similarSequences group by query_id,subject_id having count(*)>1;

          this command will give you the rows that are duplicated.

          Then you can create a new table that will have only distinct rows.

          create table holdup as select distinct * from similarSequences;
          Thanks for the help but I have a few questions:
          1. Looking at those commands I assume these are to be executed within mysql, is that correct?
          2. Will they simply replace the similarSequences table with itself with duplicates removed, or do I need to do more to be able to continue the analysis?
          3. Will this (changing the table somewhere midway the orthoMCL pipeline) not compromise the analysis?

          Thanks again!

          Comment


          • #6
            Yes, the commands have to be executed on mysql.
            first you need to select distinct rows in a different table(holdup table), delete all the rows in similarSequence table and then insert the rows from the holdup table. I hope this clears it

            Comment


            • #7
              Originally posted by jollymrt View Post
              Yes, the commands have to be executed on mysql.
              first you need to select distinct rows in a different table(holdup table), delete all the rows in similarSequence table and then insert the rows from the holdup table. I hope this clears it
              Yes, it does. Thanks very much!

              In the meantime I had redone the whole orthoMCL pipeline and for some reason got no more duplicate errors . Possibly, some table entries were accidentally copied the last time. This just to inform others that may run into the same problems..

              Comment

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