X-Envelope-to: info-gcg@utoronto.BITNET
X-VMS-To: IN%"caldwell@CWBIO.BIOC.CWRU.EDU"
X-VMS-Cc: IN%"info-gcg@utoronto",STONE
MIME-version: 1.0
Content-transfer-encoding: 7BIT
Newsgroups: bit.listserv.info-gcg
Date:         Thu, 20 Aug 1992 11:07:22 -0400
Reply-To:     Lynna Stone-Infeld <STONE@YALEMED.BITNET>
              <INFO-GCG@UTORONTO.BITNET>
From:         Lynna Stone-Infeld <STONE@YALEMED.BITNET>
Subject:      Re: Longstanding GCG problem
Comments: To: caldwell@CWBIO.BIOC.CWRU.EDU

>Dear GCG-ers:
>
>       We have a problem with our GCG package which we have been unable to
>solve.  It appears to have to do with the logical names which point to the
>libraries.  If anyone could guide me as to even where to look first for the
>errors, I would be MOST appreciative.  Thank you!
>
>                                               David Caldwell.
>
>Included is a log file demonstrating the error...
>----------------------------------------------------------------------------
>$FASTA
>
>FASTA does a Pearson and Lipman search for similarity between a
>
>query sequence and any group of sequences.  FASTA answers the
>
>question, "What sequences in the database are similar to my sequence?"
>
>The relationship between FASTA and WORDSEARCH has not been
>
>characterized, but FASTA is faster and, for some searches, more
>
>sensitive.
>
>
> FASTA with what query sequence ?
>[cavallius]wendy.pep
>
>                  Begin (* 1 *) ?
>
>                End (*    37 *) ?
>
>
> Search for query in what sequence(s) (* SwissProt:* *) ?
>genbank:*
>
> What word size (* 2 *) ?
>
>
> List how many best scores and alignments (* 40 *) ?
>
>
> What should I call the output file (* Wendy.Fasta *) ?
>[cavallius]wendy.fasta
>
> *** No sequences to compare to query sequence! ***
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
     EITHER YOUR DATABASE FILES ARE CORRUPT OR YOUR DATABASE LOGICAL IS WRONG!
     SEE BELOW


>Image data (records not beginning with "$") ignored
>$EXIT
>  CAVALLIUS    job terminated at  6-JUL-1992 13:22:13.86
>
>

David,
        You have one of two problems; 1) your GenBank database files are
corrupt or 2) your GenBank logical is not pointing at your GenBank database
files correctly.

You can check the directory GenBankDir to see if it has the appropriate files.
A clue that you may have a bad file would be if it had a different date then all
the rest of the files in that directory.

You can check what the logical name GenBank points to on your system.
You can issue the command $ SHOW LOG GENBANK then check every logical name and
file that this original GenBank logical points to. Look at the installation and
maintenance sections of the GCG System Support manual for help in understanding
the appropriate use of GenBank and other GCG logical names.

        Tracking down logical and symbol definition problems are some of the
harder things to do as a GCG system manager. They tend to take a great deal of
time and patience. The GCG technical support staff have been a great help to me
in the past with these kinds of problems even thou ultimately it was my own
stupidity of reassigning the key logical names or symbols. If you feel you are
getting nowhere fast in finding your problem try calling the GCG technical
staff.

Please let us know how you resolve this problem.

=======================================================================
- Lynna Stone-Infeld, Manager, Molecular Biology Computing Resources
                          Internet:  STONE@BIOMED.MED.YALE.EDU
                                  Bitnet: STONE@YALEMED
Biomedical Computing Unit, Yale University, School of Medicine
P.O. Box 3333, New Haven, CT, 06510
Disclaimer: my opinions are my own and may not be shared by my employer
=======================================================================
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU