pplacer/NewickError #1
Description
Hi!
Thanks a lot for developing this useful tool! I am currently trying to run it on a set of ~2,000 viral genomes.
I followed the GitHub instructions and:
- I also added prodigal to the path (otherwise I get an error)
- I had to install
ete3module to avoid 'No module found error'
However, I am now getting the following error:
Strategy:
FFT-NS-i (Standard)
Iterative refinement method (max. 2 iterations)If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.rm: cannot remove '../query_viral_genomes_protein.faa.tmp': No such file or directory
Thu Jun 20 22:54:55 CEST 2024 Replace genomes in reference trees
Running pplacer v1.1.alpha19-0-g807f6f3 analysis on Ackermannviridae_ReferenceQuery_aln.fasta...
Found reference sequences in given alignment file. Using those for reference alignment.
Pre-masking sequences... sequence length cut from 48888 to 0.
Sequence length cut to 0 by pre-masking; can't proceed with no information.
guppy: loadlocale.c:129: _nl_intern_locale_data: Assertion `cnt < (sizeof (_nl_value_type_LC_TIME) / sizeof (_nl_value_type_LC_TIME[0]))' failed.
/scratch/hb-llnext/conda_envs/vClassifier/vClassifier_family: line 314: 2631870 Aborted (core dumped) guppy tog -o "$line"_ReferenceQuery.jplace.treefile "$line"_ReferenceQuery.jplace
Traceback (most recent call last):
File "/scratch/hb-llnext/conda_envs/vClassifier/scripts/identify_monophyletic_groups.py", line 12, in
tree = Tree(args.tree_file)
^^^^^^^^^^^^^^^^^^^^
File "/home2/p304845/.local/lib/python3.11/site-packages/ete3/coretype/tree.py", line 212, in init
read_newick(newick, root_node = self, format=format,
File "/home2/p304845/.local/lib/python3.11/site-packages/ete3/parser/newick.py", line 264, in read_newick
raise NewickError('Unexisting tree file or Malformed newick tree structure.')
ete3.parser.newick.NewickError: Unexisting tree file or Malformed newick tree structure.
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.