running phredphrap

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dpaetkau
Posts: 31
Joined: Fri Jun 05, 2009 6:18 pm

running phredphrap

Post by dpaetkau » Wed Feb 22, 2012 10:59 pm

Two questions about adding new reads. We are trying to run phredphrap on multiple computers and can't get it to work. We have been adding new reads up to this point, but one computer will not do that either. I told the student to run phredphrap to incorporate the new reads, but we get the message is "command not found". I have posted the Xterminal information.
Screen shot 2012-02-22 at 8.21.48 PM.png
Screen shot 2012-02-22 at 8.21.48 PM.png (15.2 KiB) Viewed 3895 times
The second question deals with adding new reads. The one computer will not do it. We copy the chromatogram files into the chromat_dir and we copy the .fof file into the edit_dir. We check to make sure they are there. Then when students open consed, and try to add new reads they get a 512 error message. If they say Dismiss, the terminal locks up. I have pasted the screen shots to show exactly what they see.
Screen shot 2012-02-22 at 9.07.01 PM.png
Screen shot 2012-02-22 at 9.07.01 PM.png (21.79 KiB) Viewed 3895 times
Screen shot 2012-02-22 at 9.07.25 PM.png
Screen shot 2012-02-22 at 9.07.25 PM.png (12.3 KiB) Viewed 3895 times
Thank you for your help.

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: running phredphrap

Post by wleung » Thu Feb 23, 2012 2:28 pm

Because unix commands are case-sensitive, the command should be phredPhrap and not phredphrap. When you encounter a 512 error when adding new reads, the xterm you used to launch Consed typically contains additional information about the error that may help us identify the problem. Please include a screenshot of the xterm after you tried to add new reads if possible.

However, if both phredPhrap and Add New Reads failed on a single computer, then Consed may not have been installed properly. In particular, the PATH environment should contain /usr/local/genome/bin. Otherwise the shell cannot find the program phredPhrap or the addReads2Consed.perl script used by Consed to incorporate the new reads into a new assembly.

Note that the xterm indicates that you are currently using the bash shell instead of tcsh. The detail installation instructions suggests using a different shell called tcsh (see step #6 on how to change the default shell). If you prefer to use bash, you can issue the following command on the xterm to update your PATH environment variable:

Code: Select all

echo 'export PATH="${PATH}:/usr/local/genome/bin"' >> ~/.bashrc
Open a new xterm and you should now be able to access the phredPhrap script.

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