GCG7.2 and GenBank problems

Stephen Baird sbaird at mgcheo.med.uottawa.ca
Thu Dec 21 11:48:12 EST 1995

GCG sysadmin guys,

We are using  GCG ver 7.2 and for the last year we have not been able 
to update GenBank because of space problems. We have increased our 
disk capacity but I am having trouble installing the latest version of 
Genbank. I have changed the est division in the gcguserspecs file 
 to create two division est1 and est2.  Is this okay or should both 
files be combined into one est file and one division?  The problem I 
am having is that genbanktogcg or dbindex does not seem to create a 
number file for gb_est1.seq and I have tried several times. I also 
find the I cannot fetch by accession number ( so I am trying to 
install SRS). When trying to fetch an EST sequence I must specifically 
type est:locus# to get it, the locus itself will not find anything.  
I am also having trouble generating proper size .name and .number 
files for the cumulative new data with either dbindex or genbanktogcg. 
Is anyone using this version of GCG and formatting the database locally?
I noticed that the est and "new" divisions are the largest, is that a 
problem for dbindex/genbanktogcg? Does anyone have any hints about 
what I should look at to get the database up?

Every step I try in reformatting takes quite a few hours on the Sparc2 
that we have, so it has taken a couple of weeks to try several ways to 
fix this problem. Soon I will have to deal with the new accession numbers.

Thank you for any suggestions,

| Stephen Baird                        sbaird at mgcheo.med.uottawa.ca  | 
| Molecular Genetics                       tel: 613-738-3925         |
| Children's Hospital of Eastern Ontario   fax: 613-738-4833         |
| 401 Smyth Rd.                                                      |
| Ottawa, Ontario                                                    |
| Canada                                                             |
| K1H 8L1                                                            |

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