Hi,
My last Modeller job failed, and the last line of my log file is:
coutpir___E> reading in alignment
Can you tell me what 'coutpir' means ?? More generally, where can I find a list of Modeller error messages and their significances.
Thanks in advance,
Xavier Gallet, PhD Department of Bioinformatics & IT GenOdyssee S.A. 3 avenue du Canada Batiment Alpha, Porte 6 B.P. 810 Les Ulis 91974 Courtaboeuf Cedex, France
e-mail : gallet@genodyssee.com website: http://www.genodyssee.com
Similar question really.
I end up with : ipdbnam_W> environment variable PDBENT undefined rdpir___E> reading in alignment
then everything dies. I have been using modeller sucessfully for three years but for some reason this file won't run? Cheers Tim Xavier Gallet wrote:
> Hi, > > My last Modeller job failed, and the last line of my log file is: > > coutpir___E> reading in alignment > > Can you tell me what 'coutpir' means ?? > More generally, where can I find a list of Modeller error messages and their > significances. > > Thanks in advance, > > Xavier Gallet, PhD > Department of Bioinformatics & IT > GenOdyssee S.A. > 3 avenue du Canada > Batiment Alpha, Porte 6 > B.P. 810 Les Ulis > 91974 Courtaboeuf Cedex, France > > e-mail : gallet@genodyssee.com > website: http://www.genodyssee.com
-- Tim Dafforn University of Cambridge Structural Medicine Unit Cambridge Institute for Medical Research Hills Rd, Cambridge CB2 2XY. UK Tel. (01223) 763230 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/
Hello
usually the text after _E> should be informative.
there is a list of error messages, which might not be much more helpful, but you can take a look:
$MODINTALL6v0/modlib/messages.lib
in your cases the alignment format is incorrect somewhere, alignment code or sequence is not matching the top file variable or the PDB entry.
an extended log file can be obtained with
SET OUTPUT_FORMAT = 1 1 1 1 1
a very extended log file can be obtained by
SET OUTPUT_FORMAT = 1 1 1 1 2
best Andras
"T. .R. Dafforn" wrote: > > Similar question really. > > I end up with : > ipdbnam_W> environment variable PDBENT undefined > rdpir___E> reading in alignment > > then everything dies. > I have been using modeller sucessfully for three years but for some reason this > file won't run? > Cheers > Tim > Xavier Gallet wrote: > > > Hi, > > > > My last Modeller job failed, and the last line of my log file is: > > > > coutpir___E> reading in alignment > > > > Can you tell me what 'coutpir' means ?? > > More generally, where can I find a list of Modeller error messages and their > > significances. > > > > Thanks in advance, > > > > Xavier Gallet, PhD > > Department of Bioinformatics & IT > > GenOdyssee S.A. > > 3 avenue du Canada > > Batiment Alpha, Porte 6 > > B.P. 810 Les Ulis > > 91974 Courtaboeuf Cedex, France > > > > e-mail : gallet@genodyssee.com > > website: http://www.genodyssee.com > > -- > Tim Dafforn > University of Cambridge > Structural Medicine Unit > Cambridge Institute for Medical Research > Hills Rd, Cambridge CB2 2XY. > UK > Tel. (01223) 763230 > Fax. (01223) 336827 > http://smokeroom.cimr.cam.ac.uk/
Thanks for the help, Got more information, problem was missing * at end of .pri file Doohh! Tim
Andras Fiser wrote:
> Hello > > usually the text after _E> should be informative. > > there is a list of error messages, which might not be much more > helpful, but you can take a look: > > $MODINTALL6v0/modlib/messages.lib > > in your cases the alignment format is incorrect somewhere, alignment > code or sequence is not matching the top file variable or the PDB entry. > > an extended log file can be obtained with > > SET OUTPUT_FORMAT = 1 1 1 1 1 > > a very extended log file can be obtained by > > SET OUTPUT_FORMAT = 1 1 1 1 2 > > best > Andras > > "T. .R. Dafforn" wrote: > > > > Similar question really. > > > > I end up with : > > ipdbnam_W> environment variable PDBENT undefined > > rdpir___E> reading in alignment > > > > then everything dies. > > I have been using modeller sucessfully for three years but for some reason this > > file won't run? > > Cheers > > Tim > > Xavier Gallet wrote: > > > > > Hi, > > > > > > My last Modeller job failed, and the last line of my log file is: > > > > > > coutpir___E> reading in alignment > > > > > > Can you tell me what 'coutpir' means ?? > > > More generally, where can I find a list of Modeller error messages and their > > > significances. > > > > > > Thanks in advance, > > > > > > Xavier Gallet, PhD > > > Department of Bioinformatics & IT > > > GenOdyssee S.A. > > > 3 avenue du Canada > > > Batiment Alpha, Porte 6 > > > B.P. 810 Les Ulis > > > 91974 Courtaboeuf Cedex, France > > > > > > e-mail : gallet@genodyssee.com > > > website: http://www.genodyssee.com > > > > -- > > Tim Dafforn > > University of Cambridge > > Structural Medicine Unit > > Cambridge Institute for Medical Research > > Hills Rd, Cambridge CB2 2XY. > > UK > > Tel. (01223) 763230 > > Fax. (01223) 336827 > > http://smokeroom.cimr.cam.ac.uk/ > > -- > , > Andras Fiser, PhD # phone: (212) 327 7216 > The Rockefeller University # fax: (212) 327 7540 > Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu > New York, NY 10021-6399, USA # http://salilab.org/~andras
-- Tim Dafforn University of Cambridge Structural Medicine Unit Cambridge Institute for Medical Research Hills Rd, Cambridge CB2 2XY. UK Tel. (01223) 763230 Fax. (01223) 336827 http://smokeroom.cimr.cam.ac.uk/
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Andras Fiser -
T. .R. Dafforn -
Xavier Gallet