Hello,
I have run into an error in TreeSAAP on only some genes. Most are working fine, but some cause TreeSAAP to return the error "There was a problem while running tree: " and the progress bar has "Opening file progress: File: /home/Programs/TreeSAAP_3.2/rst" and "Reading file 100%, Parsing data 99%" where it stops.
It seems to be an issue reading in the baseml rst file (which is created successfully, and I can't see any obvious issues in it). The verbose output from GeneralDNAFileParser.java and TreeControl.java seems to suggest that it is erroneously grabbing the "Check root of tree for directions of change." and subsequent Branch amino acid change information, so it never manages to associate those branches with the tree correctly. But that line also exists in rst files from genes that do work, and it isn't grabbed by TreeControl.java, so I don't know what's up.
Any ideas? Or is there a way to run TreeSAAP from an existing rst file (so I could perhaps delete that troublesome line and hope it helps)?
Thank you. Elise
You have to use a compiled BaseML executable that is compiled from the PAML 3.14 source code on your running machine (or at least your flavour of LINUX/UNIX). You can get the PAML 3.14 from here: http://abacus.gene.ucl.ac.uk/software/pamlOld.html
Follow the compile (MAKE) instructions and then copy the <baseml> executable back into the BASEML directory of TreeSAAP.