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<TITLE>Re: [maker-devel] GeneMark HMM</TITLE>
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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hello,<BR>
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I’m going to run a few tests, and see if I can replicate the error first. Then I’ll try a few workarounds. I may even need to update the maker code, i.e. Have GeneMark write to the /tmp directory and then on completion copy this short location to where I really want the output to be.<BR>
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One suggestion for now. You said you are running GeneMark.hmm eukaryotic. So you are not using GeneMark-ES. Am I correct? If you are not using GeneMark-ES, try downloading GeneMark-ES which contains a version of GeneMark.hmm internally that is newer than the version of GeneMark.hmm contained in the GeneMark.hmm download. This may seem confusing, but when you go to the GeneMark download page, they ask you if you want GeneMark-ES or GeneMark.hmm.<BR>
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If this suggestion fixes your problem, please let me know. I’ll let you know when I’ve come up with a workaround.<BR>
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Thanks,<BR>
Carson<BR>
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On 7/16/09 7:29 AM, "Xavier Watkins" <<a href="xavier@flymine.org">xavier@flymine.org</a>> wrote:<BR>
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</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><FONT SIZE="1"><SPAN STYLE='font-size:9pt'>Hi there,<BR>
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I've recently started using Maker and it's great! <BR>
I've got RepeatMasker, Snap and Blastall working fine but I'm having problems with GeneMark HMM. I think the problem comes from the fact it doesn't seem to like output file paths longer than about 90 characters... <BR>
When I run it from the command line I get "ehmm: error in command line" but when I reduce the length of the -o path it runs fine. As the path generated by maker is quite long, I was wondering if you had come across this problem and found a workaround? I'm running GeneMark.hmm eukaryotic on LINUX 64.<BR>
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Many thanks,<BR>
Xavier<BR>
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