In article <2o18ks$b0v at mserv1.dl.ac.uk>, "A. Kalogeropoulos" <angelos at igmors.u-psud.fr> writes:
|>|> >
|> > *** Error: Cannot open file FUN:SCCHROMI
|> >
|> >
|> >
|> > What is the cause of this error ?
|> >
|>|> You have to specify EM_FUN:SCCHROMI (and not FUN:SCCHROMI)
|>
Check the following first:
1 . cd $GCGSYSTEMROOT/gcgcore/data/rundata
check that the file dbnames.map has the following entries
for embl:
inv em_in in ! embl invertebrate
phg em_ph ph ! embl bacteriophage
fun em_fun pl ! embl fungi
org em_or or ! embl organelle
mam em_om om ! embl other mammal
vrt em_ov ov ! embl other vertebrate
pln em_pl pl ! embl plant
pri em_pr pr ! embl primate
pro em_ba ba ! embl prokaryote
rod em_ro ro ! embl rodent
syn em_sy sy ! embl synthetic
unc em_un un ! embl unannotated
vrl em_vi vi ! embl virus
bb em_bb ! embl backbone sequences
patent em_pat pat ! embl patent sequences
est em_est est ! embl est sequences
2. check that embl.farm corresponds with this file.
3. If the above is a hassle make sure to check the header files
on the gcgdata/gcgembl directory. My bet is that there is something
unspecified here, like embldir:fu. If this is true it should read
embldir:em_fun. The long name and short names can be FUN and FU if
you like, but fasta reads the full name for retrieval during
the alignment step.
Hope this helps.
--
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