Hi Melanie, The warning message you get is referring to running an external program to Artemis (rather than an external site). You can ignore it or change etc/log4j.properties¹ and remove the #¹ at the start of the line:
log4j.logger.uk.ac.sanger.artemis.ExternalProgram=DEBUG, R To get error messages open the Show Log Window¹ in the Options¹ menu in the initial start up window in Artemis. It may prove easier to debug the script by running it from the command line, e.g.: etc/run_blastp blastp/blastp_file_of_filenames.18 %U For the control+V problem, I haven¹t seen that before. What flavour of UNIX are you using and what version of Java? You could try getting the latest Java if you haven¹t already. Regards Tim Carver On 20/2/08 08:57, "Duffield Melanie L" <[EMAIL PROTECTED]> wrote: > Hi, > I am trying to get Artemis v9 set up on a networked Unix computer (or at > least co-ordinate with our IT people to do this). I have it running locally > on a stand-alone but we want to make it more widely available. I now have > Artemis runnng but still have some problems. > > Firstly, I get the messages > log4j:WARN No appenders could be found for logger > (uk.ac.sanger.artemis.ExternalProgram0. > log4j:WARN Please initialize the log4j system properly. > > Due to our firewire, we can not set up the program to access any external > sites so is there a way to remove this message? > > Secondly I am trying to get blast searches to run. We have local databases > set up under a directory that runs the local windows version of blast and the > blastall is located in the standalone program version. I have edited options > and run_blastp to these two address. > > When I start a Blastp search, the sequence file is written out to the blastp > directory and the message 'blastp process received signal: 2 Ok' comes up but > there is no .out file and it seems that blastp doesn't actually run. Is there > any way to see error messages (ie if it can't find or access the database or > blastall). I have checked for typos and access problems and cant see anything > obvious. > > Finally, when I use control V to view selected feature, the dialogue box is > put behind the main Artemis window, can I change the default some where to > open it at the front. > > Apologies that there are so many questions but maybe someone out there has > seen something like this before and knows the fixes? > > Thanks in advance > > Melanie Duffield > Team Leader - Advanced DNA and Protein Technologies > Dstl > Rm 201, Bld 7a > Porton Down > Wilts > SP4 0JQ > > +44 (0) 1980 614364 > > "The Information contained in this E-Mail and any subsequent correspondence" > "is private and is intended solely for the intended recipient(s)." > "For those other than the recipient any disclosure, copying, distribution, " > "or any action taken or omitted to be taken in reliance on such information > is" > "prohibited and may be unlawful." > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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