[phenixbb] error message running example
Tom Terwilliger
terwilliger at lanl.gov
Wed Nov 7 13:49:58 PST 2007
Hi Norman,
I'm very sorry for this problem! I am puzzled...it sounds like somehow
SOLVE cannot write to the directory it is working in. (I have never seen
this one before!)
Can you try this: go to your home directory, make a subdirectory "test"
there, get in the directory, and copy $PHENIX/examples/nsf-d2-sad/peak.sca
to this subdirectory. Then run autosol by hand. Then (fail or not) do an
ls -lt to show what the permissions are. Like this:
cd
mkdir test
cd test
cp $PHENIX/examples/nsf-d2-sad/peak.sca .
phenix.autosol peak.sca quick=True build=False debug=True |tee test.log
ls -lt
If this works (you'll know because it gets past scaling and starts doing
phasing)...it is file permissions of some sort. If it fails, hopefully
something in test.log or AutoSol_run_1_/LAST.log or the "ls -lt" output
will tell me something...
Thank you!
-Tom T
ps. I did get your email yesterday on the help BB, but I replied to
an incorrect email address. I'm sorry about that too!
At 06:01 AM 11/7/2007, you wrote:
>Content-class: urn:content-classes:message
>Content-Type: multipart/alternative;
> boundary="----_=_NextPart_001_01C8213E.3EA9AF22"
>
>Hi -
>
>I tried to run the example:
>phenix.run_example gene-5-mad
>
>However, it stopped, with following error messages:
>
>Done with gene-5-mad ...Your results are in the directory:
>gene-5-mad/AutoSol_run_1_
>Missing the summary file: gene-5-mad/AutoSol_run_1_/
>Something did not work properly...not all output files produced
>
>and the LAST.LOG reports:
>
> ***************************************************************************
> 6769 SOLVE STATUS 07-nov-07 12:47:15
> 6770
> 6771 DATASET TITLE:
> SOLVE 07-Nov-07 STATUS
> 6772 STATUS: UNABLE TO FIND UNIQUE NAME FOR SCRATCH
> 6773
> ---------------------------------------------------------------------------
> 6774 Sorry -- ERROR ENDING. SEE the end of your log file or
> output STATUS
> 6775 and solve.log
> 6776 for more information STATUS
>
>Any idea what is going wrong? (phenix version 1.3 beta rc4, 64bit
>computer, 2 dual core proc.)
>
>Many thanks,
>
>Norman
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>phenixbb at phenix-online.org
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web
site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
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