gap4 database is not consistent (anno tag)

  • Hi,

    I used staden Version 1.7.0 and have a problem with an inconsistent
    database (gap v4.11);
    "Annotation 153: Neither used or free. Database is not consistent. 1
    minor problems detected." (Check database output)

    Trying to solve the problem with the tools from Doctor database:
    "Output annotations to file" --> anno_list, but no. 153 is not in
    there (it's an OLIG tag).

    Then I created a anno_list file manually with the position, length
    etc found in "output annotation" (no 153) and deleted the annotation
    ("Delete annotation")

    This does nothing; problem is still present.

    copy_db with the "fix switch" (-f) on didn't make it neither.

    Any idea what to do ?

    • María José
      María José

      I have "7 minor problems detected" in my database like you, and I did the same that you too, but the problems are still. I don´t Know what to do more!!!

    • Sven Klages
      Sven Klages

      The problem might be solved with the CAF tools from Sanger Centre.

      - convert GAP to CAF (gap2caf)
      - convert back to GAP (caf2gap)

      This fixed every "inconsistency problem" I had .. :-)



    • María José
      María José

         Dear Sven:
         Thanks a lot for your advice!! now my database is consistent!!!
         Best regards;-)