Error in pan-genome-analysis tool panX.

Question

[Kumar]

I have been using panX tool for pan-genome analysis (My computer info: Ubuntu 16.04 LTS, 64 bit version). I followed the instructions mentioned in the manual and installed all the dependencies (mcl, mafft, fastree, raxml, DIAMOND, treetime). After that, I ran the test as mentioned in the tool manual and end up with the following error,

mv: cannot stat 'GC00000142_aa_aln.fa': No such file or directory
mv: cannot stat 'GC00000142_na_aln.fa': No such file or directory
mv: cannot stat 'GC00000364_aa_aln.fa': No such file or directory
mv: cannot stat 'GC00000364_na_aln.fa': No such file or directory
mv: cannot stat 'GC00000322_aa_aln.fa': No such file or directory
mv: cannot stat 'GC00000322_na_aln.fa': No such file or directory
mv: cannot stat 'GC00000172_aa_aln.fa': No such file or directory
mv: cannot stat 'GC00000172_na_aln.fa': No such file or directory
mv: cannot stat 'GC00000217_aa_aln.fa': No such file or directory
mv: cannot stat 'GC00000217_na_aln.fa': No such file or directory
Traceback (most recent call last):
  File "./panX.py", line 303, in <module>
    myPangenome.build_core_tree()
  File "/home/dinesh/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 "/home/dinesh/pan-genome-analysis/scripts/sf_core_tree_build.py", line 44, in aln_to_Newick
    resolve_polytomies('initial_tree.newick0','initial_tree.newick')
  File "/home/dinesh/pan-genome-analysis/scripts/sf_core_tree_build.py", line 8, in resolve_polytomies
    tree = Tree(newickString);
  File "/home/dinesh/.local/lib/python2.7/site-packages/ete2/coretype/tree.py", line 218, in __init__
    read_newick(newick, root_node = self, format=format)
  File "/home/dinesh/.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.

As an alternative option this tool can be ran in miniconda environment (mentioned in the manual), therefore I have tried the same but end up with the identical error as mentioned above. Please help me to fix this issue.

[GenoMax]

Error appear to be informative. You are missing a bunch of aligned (?) data files (at least they must not be in your $PATH). And that probably leads to a non-existing tree file.

[Kumar]

Thank you @genomix. However the test script itself showing this kind of error. I could not find out the way to fix it.