diff --git a/ipyrad/analysis/treeslider.py b/ipyrad/analysis/treeslider.py index 8c7459be..0c1fe907 100644 --- a/ipyrad/analysis/treeslider.py +++ b/ipyrad/analysis/treeslider.py @@ -341,7 +341,7 @@ def _init_tree_table(self): "sites": 0, "samples": 0, "missing": 0.0, # np.nan, - "tree": 0, + "tree": "", }, columns=[ "scaffold", "start", "end", @@ -459,7 +459,7 @@ def _run(self, force=False, ipyclient=None): for idx in self.tree_table.index: # if continuing an existing job, skip if row already filled - if self.tree_table.tree[idx] != 0: + if self.tree_table.tree[idx] != "": prog.finished += 1 continue @@ -593,8 +593,7 @@ def remote_mrbayes(nexfile, inference_args, keepdir=None): def remote_raxml(phyfile, inference_args, keepdir=None): - """ - Call raxml on phy and returned parse tree result + """Call raxml on phy and returned parse tree result """ # if keep_all_files then use workdir as the workdir instead of tmp if keepdir: @@ -613,9 +612,9 @@ def remote_raxml(phyfile, inference_args, keepdir=None): # get newick string from result if os.path.exists(rax.trees.bipartitions): - tree = toytree.tree(rax.trees.bipartitions).newick + tree = toytree.tree(rax.trees.bipartitions).write() else: - tree = toytree.tree(rax.trees.bestTree).newick + tree = toytree.tree(rax.trees.bestTree).write() # remote tree files if keepdir is None: