[Bio-Linux] Pregap4/Gap4 problems

[Bela Tiwari]

Hi Jose,

Luckily, this is a very easy problem to solve. It also happens frequently, so save this answer somewhere.  :-)

Gap4 creates a file with a suffix of .BUSY   when someone opens a particular database. For example, if you named your database  testdb, and you only have one version, the database will be called testdb.0.aux. The file you want to delete is called testdb.0.BUSY.  

Creating a file like this is a very basic way of trying to stop people working on the same database simultaneously and overwriting each others work. This file is deleted when gap4 is shut down. Unfortunately, if gap4 isn't shut down properly, this file doesn't get deleted and when you next try to open the database, gap4 thinks someone is already working on it. 

The solution, as you have probably already guessed is:  delete the   BUSY file. 


cheers

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> jaa53 at cornell.edu 12/12/2006 15:16 >>>
Hi all,

I am using pregap4/gap4 to assemble a BAC and I have problems adding  
sequences to to an existing database....

When running pregap4 (Phrap assembly) I get the following error  
"database busy" (even if no one is using it!) I have deleted  
the .BUSY file and run pregap again. This time I do not get any  
errors but the sequences that passed are not added (the new sequences  
are not into the pregap.assembly directory even if the pregap4 output  
window reads "assembled data written to directory ../pregap.assembly"  
and no error messages are generated). Any idea of what is going on?    
Any suggestions?

  -- I am at the beginning of the project and most of the sequences I  
have are singlets (can that be part of the problem?) ---


Thanks in advance,

/Jose


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