Hi Nicole This may well be just Artemis running out of memory. It has to read in the entire file and it is likely that it may be running out of memory before it can display the data. I have changed the code so that it will warn you if this happens this will appear in the next release of Artemis.
I would recommend you try increasing the memory allocated to Artemis on your machine. Have a look at FAQ no. 4 to on increasing memory: http://www.sanger.ac.uk/Software/Artemis/faqs.shtml#tips Regards Tim On 2/11/08 03:55, "Nicole Cloonan" <[EMAIL PROTECTED]> wrote: > > Hello, > > I have started using Artemis for the first time as a way to overlay next-gen > sequencing data onto annotated bacterial genomes. It has the capability of > doing everything that I need it to do, but I am having trouble with my own > custom user plots. It is probably something that I am doing wrong, but I just > can't seem to figure it out on my own! Any clues would be greatly appreciated. > > I am using Artemis 10 standard release, with Java 6 update 10, on Window XP > professional SP 2, fully updated. > > Artemis appears to be working well. To confirm this I downloaded the > supplementary data from http://www.biomedcentral.com/1471-2164/9/364, and I > was successfully able to open and view the custom user plots on the provided > gbk file. > > However, I am unable get my own custom user plots to be successfully opened in > Artemis. I am creating these on a separate machine (running RHEL 5), copying > the space delimited format seen in the above data set. I do not get any error > messages, the plots just don't display. I think this might be an EOL/encoding > issue because if I attempt to modify the user plots downloaded above (using > either word, notepad, wordpad, or excel but saving as "text"), then these also > fail to load. > > I have tried without success: > > * renaming the file > * unix2dos before binary transfer to the windows box. > * unix2dos before ascii transfer to the windows box. > * opening the file using windows/word/notepad/excel and pasting/saving to a > new text file. > > According to the "file" program on unix, the downloaded data and the post > unix2dos custom data have the same encoding, so I don't really know where to > go from here. I have been through Google, and through the archives for this > mailing list without success - so either I am doing something completely > moronic, or no one else in the world is having this issue! Any > help/suggestions/flames (do people still say "flame"? =) ) would be greatly > appreciated. I need to get this working on a Windows system, because that's > what the end users of this data will be using. > > Cheers, > Nicole. > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
_______________________________________________ Artemis-users mailing list [email protected] http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
