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
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 ?
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!!!
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 .. :-)
Thanks a lot for your advice!! now my database is consistent!!!