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  • Error with Repeat Modeler

    Hello,

    I am working on Repeat annotation of A. indica (Neem).
    While using Repeat Modeler, it runs for 6 rounds on my scaffolds file(118093 sequences).

    In the 6th round at about 14% it stops, with NO error.
    On further investigation the Error log file shows an Floating Point error in the 5th round.
    And the working directory contains a file called as "consensi.fa".

    Now while the on line documentation for Repeat Modeler mentions the final output file to be called as "consensi.fa.classified" which is not there I have "consensi.fa".
    Has the Repeat Modeler run gotten over properly?
    Can I use this file for downstream repeat analysis?

    Regards,
    --
    pg

  • #2
    Hello,

    Should I use the "consensi.fa" file for further analysis, has the run got over properly?
    Can anyone provide an insight?

    --
    pg

    Comment


    • #3
      Solved

      Hi,

      No you can not use the "consensi.fa" file as the final result file.

      I just took the top 500 scaffolds from my input file and ran Repeat Modeler on them.
      It worked and produced a "consensi.fa.classified" file, no errors and the last round completed 100%.
      Now trying to determine the maximum number of scaffolds that can be processed by Repeat Modeler without any error.

      But now even if I split my input file into say 10 chunks, and get 10 "consensi.fa.classified", then all of them will have to be combined into a single file.
      IF I simply concatenate them, them there will be many redundant sequences, hence I think the best strategy is to do a, all vs. all similarity search using something like vmatch, lastz or bastn. Then remove all sequences with more than 80% similarity and a very high e-value.

      Is that a correct methodology?

      Regards,
      --
      pg

      Comment

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