Newick
Closed this issue · 7 comments
Hi - I'm running into an error during step 8. Please see output below. Any suggestions how to fix this error?
Best wishes,
Markus
====== starting step08: run fasttree and raxml for tree construction
fasttree time-cost: 0.00 minutes (0.01 seconds)
Traceback (most recent call last):
File "./panX.py", line 303, in
myPangenome.build_core_tree()
File "/media/LargeStorage/Markus_cold_adaptation-master/pangenomeanalysis/pan-genome-analysis/scripts/pangenome_computation.py", line 200, in build_core_tree
aln_to_Newick(self.path, self.folders_dict, self.raxml_max_time, self.raxml_path, self.threads)
File "/media/LargeStorage/Markus_cold_adaptation-master/pangenomeanalysis/pan-genome-analysis/scripts/sf_core_tree_build.py", line 44, in aln_to_Newick
resolve_polytomies('initial_tree.newick0','initial_tree.newick')
File "/media/LargeStorage/Markus_cold_adaptation-master/pangenomeanalysis/pan-genome-analysis/scripts/sf_core_tree_build.py", line 8, in resolve_polytomies
tree = Tree(newickString);
File "/home/markusd/.local/lib/python2.7/site-packages/ete2/coretype/tree.py", line 218, in init
read_newick(newick, root_node = self, format=format)
File "/home/markusd/.local/lib/python2.7/site-packages/ete2/parser/newick.py", line 231, in read_newick
raise NewickError('Unexisting tree file or Malformed newick tree structure.')
ete2.parser.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
this is probably an error in tree building. In the past, this has been caused by non-standard characters in strain names or too diverse data set without a core genome.
Could the version of ete2 be a case for this error?
I'm referring to ete2 or ete3...
Your initial suggestion was correct. I did not find obvious differences between files but after adding one file at the time to the pipeline, I discovered five compromised .gbk. Analysis runs fine without these files. Thanks again for your support!
good to hear and sorry about the hassle. I know we need to work on error messages and sanity checks...
No worries, We all are busy and sometime it takes days or weeks to respond.
Also realized the other day that the requirements.txt file you provided would have answered my questions about the version of ete. So, i have to apologize for not doing my homework first :)
Hi. Get this same errror while running the test data set. I am using Linux Mint 19.3 Cinnamon, and running from an anaconda python2 environment.