I get an error

[Lanre Showunmi]

I am trying to run the program from command prompt, but I keep getting "Cant find the file. I give up" message. I followed the direction exactly, please help anyone

Thanks,

Larry

[pamel...@hotmail.com]

This has happened to me and my running nssites ctl file was corrupted. If the names and the format of the files are correct, it is perhaps, then just put the data into a new model file.

[Ziheng]

i suspect this is an issue of lackign basic computer skills, especially about files and folders etc.
suppose you cd to the paml4.7/ folder. there is a control file codeml.ctl

cd paml4.7

more codeml.ctl

this control file specifies the names of the data files

seqfile = stewart.aa * sequence data filename
treefile = stewart.trees * tree structure file name

when you dir (ls) you can see that the two files stewart.aa and stewart.trees are in the current folder. then you run the program

bin\codeml (on windows)

bin/codeml (on linux or macos)

and everything will be file.

if your data files are in a different folder, you need modify the control file to specify the correct path and file name. Suppose you are currently in paml4.7, and the data file is in mtprim9.nuc in the folder paml4.7/examples/. then you should have

seqfile = examples/mtprim9.nuc * sequence data filename

if you plan to run the program in the folder paml4.7. The path examples/ is relative, starting from the current folder paml4.7.

here is an online tutorial: Windows Command Prompt in 15 Minutes
http://www.cs.princeton.edu/courses/archive/spr05/cos126/cmd-prompt.html

if you use maxos, here is another one

http://blog.teamtreehouse.com/introduction-to-the-mac-os-x-command-line

ziheng

[Alan Soffan]

Dear Ziheng

I am trying to run PAML CODEML in MacOSx, well it seem  quite different as compare to window. In Window OS I can run codeml at any folder containing my datafiles (ctl, tree and seq file) as long as I typed codeml followed by the file name (.ctl). (I can name the ctl file with any name and also without moving the dat folder).

In MacOS, based on your explanation above we have to modify the codeml.ctl file (particularly in seqfile information to locate our datafiles, if our data files in different folder, and the ctl file should always named as codeml.ctl),

My question then, is there any way to run "bin/codeml" while our ctl file named differently such as trial.ctl istead of codeml.ctl ( i tried it but it alwasy show could not find codeml.ctl file)

Thanks

[Ziheng]

macos is a variant of unix and it is very similar to windows command line.  you use / on mac and \ on windows when specifying the path or folder.  

make sure you run the program in a command line box.  i think it is called Terminal on mac.

you can run codeml like this

codeml trial.ctl

codeml ../trial.ctl

inside codeml.ctl you can specify the full path and names of the sequence alignment file and tree file.  

there are lots of online tutorials about mac or windows command line.  here are some intro materials i prepared for my course.

http://abacus.gene.ucl.ac.uk/software/CommandLine.Windows.pdf
http://abacus.gene.ucl.ac.uk/software/CommandLine.MACosx.pdf

ziheng