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.
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