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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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Creating new configuration blocks fail #682

Open Zefeng-Wu opened 1 year ago

Zefeng-Wu commented 1 year ago

When I used " iqtree_bestmodel" in species tree building, it gave an error after running for some minutes, and it reminded me that the "-safe" option should be added in iqtree command. So I create new configuration blocks by ete3 build dump iqtree_bestmodel > myconfig.cfg and I add an extra option of iqtree with "-safe=" in my configf files as followings:

[iqtree_bestmodel]
                                   -alrt = 1000
                                      -m = TESTNEWONLY
                                   -safe = 
                                   -seed = 31416
                                    _app = iqtree
                                   _desc = IQTree

Then I rerun ete-build with -c myconfig.cfg, it can not run with an error : ete3.tools.ete_build_lib.configobj.ConfigObjError: Parsing failed with several errors. First error at line 532.

So how can I add the "-safe" option in my iqtree_bestmodel setup? Thanks