In addition to the minor problems related with Annotations that are neither used or free, I got serious problems that impede the program to do must of their functions... but I do not find how to fix them with Doctor Database or even checking by hand.
One of my Check messages says "Annotation 743: Pos (127), leftwards of previous tag 234 (Pos 678)". I see tag 234, but nothing appears in position 127 of the same contig...
Another message says "Annotation 456: loop detected in free list"
Any clue about how to solve these?
Thanks a lot.
The copy_db command line utility can fix some problems. Use "copy_db -v -f dbname.0 dbname.1" (for example).
How did you get the annotation errors though?
The copy_db didn't fix the problem we had.
I have no idea how these errors were introduced. A colleague of mine
was working on a relatively small DB, something like 60 EST clones. He
was putting oligo tags (and some comment tags) on the sequences when
he reported me the inconsistencies.
AFAIR we had these inconsistencies from time to time, in every version
of gap4. We could almost always fix the problems with the CAF tools :-)
As we changed from gap4 to consed a few years ago, I don't have extensive
experience with the current versions of gap4, as I do use it only sporadically.