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URGENT help FASTA on GCG

Charles Bailey bailey at hmivax.humgen.upenn.edu
Fri Apr 8 03:24:19 EST 1994


In article <2o12d2$59h at mserv1.dl.ac.uk>, <LIUNI at PLAUTO.CSATA.IT> writes:
>  FASTA with what query sequence ?  p.seq
> 
>                   Begin (* 1 *) ?
>                 End (*   145 *) ?
> 
>  Search for query in what sequence(s) (* GenEMBL:* *) ?  em_fun:*
> 
>  What word size (* 6 *) ?
> 
>  List how many best scores and alignments (* 40 *) ?
> 
>  What should I call the output file (* P.Fasta *) ?
> 
>           1 Sequences         378 bp searched    FUN:A00040
>         101 Sequences     143,453 bp searched    FUN:ANACUD

This is a bit odd - the usual GCG configuration uses the logical name Em_Fun to 
access these files.  However, you are able to read the sequence data, so I
suspect it's a configuration quirk at your site.  Checking logical names may
elucidate this, FWIW.

> The best scores are:                                        init1 initn opt
> 
> 
>  *** Error: Cannot open file FUN:SCCHROMI

We've established previously that you can read the sequence data, but you're
now having problems reading the locus definition line.  I'd guess that you have
a file protections problem in EMBLDir: (e.g. the .Ref file is not readable from
the account which is running FASTA), or that some of your libary files are
corrupted.  If you try 
$ Fetch Fun:SCCHROMI
what results do you get?

                    Regards,
                    Charles Bailey

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