Error: end of tree file.. paml-4.10.6

[Lala]

Hello,  

I've been trying to learn to use codeml with paml-4.10.6 but the run always stops after the first gene in my seqs file with, "Error: end of tree file.."  I've tried reformatting files a million times to no avail.  

Since I'm just trying to learn I have no idea what I'm getting wrong!

I eventually installed EasyCodeML hoping it would give me errors I could more easily interpret.  Instead, EasyCodeML (running paml-4.9) worked without any errors. I've also confirmed that the build of paml-4.8 runs fine on my machine.  Both of those runs were using the same files that failed with v4.10.

I am working on a Mac running Mojave.  When I initially compiled paml 4.10 I had received errors that I didn't really understand and i decided to ignore them (warning: unknown warning option '-Wmemset-elt-size'; did you mean '-Wvec-elem-size'? [-Wunknown-warning-option]).  I had the same issue if I tried to compile it with CC or GCC.  Yesterday while pouring over this site I found another mention of this error so following their lead I also removed that item (-Wmemset-elt-size) from the CFLAGS in the Makefile and rebuilt.  Unfortunately I'm still getting the same error when I try to run codeml with paml-4.10.6.

So ultimately the issue seems to be with compiling 4.10 but not sure of the way forward.  

Thanks,

Laura

[Janet Young]

hi Laura,

two ideas:

First, I think I got the same error when I updated recently to 4.10 and in my case it turned out to be because 4.10 is more picky about the exact format of the tree file. I also got the "Error: end of tree file.." message .  With 4.10 you need to make sure the first like of your tree file is not the tree itself, but two numbers - number of species, then number of trees. See page 15 of the manual: http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf.    Version 4.9 was able to handle tree files without this first line, but 4.10 requires the first line.

Second, I think the above will probably fix things for you, but if you still need to troubleshoot installation, it is probably better to use example files provided in the PAML download, instead of your own seq+tree inputs, just in case there is something weird about your files.

Hope one of those works!

Janet

[Lala]

Hi Janet, and thank you so much!!  That was indeed the issue! 

And you are absolutely right I should have used the example files first.  I did run through the examples and later tried to find differences between our files, but looking back now, I realize that I ran the example I ran was when I was still using the 4.9 instal.  Ahha!

Many thanks,

best,

Laura