Error running treetime; RecursionError: maximum recursion depth exceeded while calling a Python object

[jsan4christ]

Hallo TT team,

I'm getting this error running treetime locally on my Mac and on the server (CentOS 7).

treetime clock --tree new_tree3.nwk --dates dates.csv --aln nextalign.aligned.new_tree3.fasta --reroot "oldest"

0.00 -TreeAnc: set-up

Attempting to parse dates...
Using column 'strain' as name. This needs match the taxon names in the tree!!
Using column 'date_decimal' as date.

391.48 TreeTime.reroot: with method or node: oldest

448.94 TreeTime.reroot: with method or node: oldest

485.78 TreeTime.reroot: with method or node: oldest

Root-Tip-Regression:
--rate: 2.431e-03
--r^2: 0.58

The R^2 value indicates the fraction of variation inroot-to-tip
distance explained by the sampling times.Higher values corresponds
more clock-like behavior (max 1.0).

The rate is the slope of the best fit of the date tothe root-to-tip
distance and provides an estimate ofthe substitution rate. The rate
needs to be positive!Negative rates suggest an inappropriate root.

The estimated rate and tree correspond to a root date:

--- root-date: 2020.35

Traceback (most recent call last):
File "/Users/sanem/miniconda3/envs/nextstrain/bin/treetime", line 12, in
return_code = params.func(params)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/treetime/wrappers.py", line 1056, in estimate_clock_model
Phylo.write(myTree.tree, outtree_name, 'newick')
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/_io.py", line 77, in write
n = getattr(supported_formats[format], "write")(trees, fp, **kwargs)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 61, in write
return Writer(trees).write(handle, plain=plain, **kwargs)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 260, in write
for treestr in self.to_strings(**kwargs):
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 308, in to_strings
rawtree = newickize(tree.root) + ";"
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 301, in newickize
return "(%s)%s" % (",".join(subtrees), label + make_info_string(clade))

--

File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 300, in
subtrees = (newickize(sub) for sub in clade)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/site-packages/Bio/Phylo/NewickIO.py", line 293, in newickize
unquoted_label = re.match(token_dict["unquoted node label"], label)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/re.py", line 172, in match
return _compile(pattern, flags).match(string)
File "/Users/sanem/miniconda3/envs/nextstrain/lib/python3.6/re.py", line 289, in _compile
p, loc = _cache[type(pattern), pattern, flags]
RecursionError: maximum recursion depth exceeded while calling a Python object

What have I tried?

• Check that alignment, tree and dates are in sync
• Update treetime from 0.8.6 to 0.9.0 to 0.9.1
• Remove and re-install nextstrain conda environment and treetime.

None has worked. Is there something I'm missing?

NB: A colleague was able to run the same command on the same data on his computer and it worked fine.

Please advise

[rneher]

Hi San,

this has to do with the cap on recursive function calls. In augur, we have a way to set it via environment variables. but this is currently not implemented in treetime proper. I'll add this to treetime as well. Beyond that, there is not much I can do since this error happens when Biopython converts the tree to newick.

best,
richard

[jsan4christ]

Right, thanks for the response. I totally understand.

Please do let me know when the change is implemented.

Regards.