From jaa53 at cornell.edu Tue Dec 12 10:16:07 2006 From: jaa53 at cornell.edu (Jose Andres) Date: Tue, 12 Dec 2006 10:16:07 -0500 Subject: [Bio-Linux] Pregap4/Gap4 problems Message-ID: <7E4D14D6-112C-4FDE-8FFE-CE6EEB72FE5E@cornell.edu> 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 From btiwari at ceh.ac.uk Tue Dec 12 10:25:54 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Tue, 12 Dec 2006 15:25:54 +0000 Subject: [Bio-Linux] Pregap4/Gap4 problems Message-ID: 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 _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From btiwari at ceh.ac.uk Tue Dec 12 10:52:44 2006 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Tue, 12 Dec 2006 15:52:44 +0000 Subject: [Bio-Linux] Pregap4/Gap4 problems Message-ID: Hi Jose, My apologies - I should have read your question more carefully. You know about the BUSY file for gap4. And gap4 isn't even your problem. Okay - re-reading your question more carefully this time (!), I think this is one for the helpdesk as I'm not sure from what you wrote whether the problem is rooted in how you are trying to use phrap, or pregap4 itself, or.... I'll start up a helpdesk ticket for this now and we can continue our conversation there. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 *************************