Closed nohayoussef closed 6 years ago
Hello Noha. Looks like the taxonomy strings in your Newick tree do not form a 7 rank taxonomy. If you are looking to classify genomes according to the methodology used by the GTDB, I recommend using our companion tool GTDB-Tk instead of PhyloRank.
Thanks Donovan. Will do. Noha
Sent from my iPhone
On Jul 16, 2018, at 7:04 PM, Donovan Parks notifications@github.com wrote:
GTDB-Tk
Hello, While running phylorank to first decorate a tree then calculate RED using the below commands phylorank decorate /scratch/nohayous/ForAnvio/tree_all.nwk /scratch/nohayous/ForAnvio/taxonomy_PR.txt /scratch/nohayous/ForAnvio/tree_all_dec.nwk --skip_rd_refine phylorank outliers /scratch/nohayous/ForAnvio/tree_all_dec.nwk /scratch/nohayous/ForAnvio/taxonomy_PR.txt /scratch/nohayous/ForAnvio/Phylorank
I got the following error: /opt/anaconda/4.0.0/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') [2018-07-10 15:39:21] INFO: PhyloRank v0.0.37 [2018-07-10 15:39:21] INFO: phylorank decorate /scratch/nohayous/ForAnvio/tree_all.nwk /scratch/nohayous/ForAnvio/taxonomy_PR.txt /scratch/nohayous/ForAnvio/tree_all_dec.nwk --skip_rd_refine [2018-07-10 15:39:21] INFO: Reading tree. [2018-07-10 15:39:21] INFO: Removing any previous internal node labels. [2018-07-10 15:39:21] INFO: Reading taxonomy. [2018-07-10 15:39:21] INFO: Calculating F-measure statistic for each taxa.
Unexpected error: <type 'exceptions.IndexError'> Traceback (most recent call last): File "/opt/anaconda/4.0.0/bin/phylorank", line 350, in
parser.parse_options(args)
File "/opt/anaconda/4.0.0/lib/python2.7/site-packages/phylorank/main.py", line 453, in parse_options
self.decorate(options)
File "/opt/anaconda/4.0.0/lib/python2.7/site-packages/phylorank/main.py", line 226, in decorate
options.output_tree)
File "/opt/anaconda/4.0.0/lib/python2.7/site-packages/phylorank/decorate.py", line 537, in run
fmeasure_for_taxa = self._fmeasure(tree, taxonomy)
File "/opt/anaconda/4.0.0/lib/python2.7/site-packages/phylorank/decorate.py", line 70, in _fmeasure
extent_taxa_with_label[i] = Taxonomy().extant_taxa_for_rank(rank, taxonomy)
File "/opt/anaconda/4.0.0/lib/python2.7/site-packages/biolib/taxonomy.py", line 661, in extant_taxa_for_rank
if taxa[rank_index] != Taxonomy.rank_prefixes[rank_index]:
IndexError: list index out of range
[2018-07-10 15:39:22] INFO: PhyloRank v0.0.37
[2018-07-10 15:39:22] INFO: phylorank outliers /scratch/nohayous/ForAnvio/tree_all_dec.nwk /scratch/nohayous/ForAnvio/taxonomy_PR.txt /scratch/nohayous/ForAnvio/Phylorank
[2018-07-10 15:39:22] ERROR: Input file does not exists: /scratch/nohayous/ForAnvio/tree_all_dec.nwk
Controlled exit resulting from an unrecoverable error or warning.
I am not sure what's going on. Could you possibly help with that?
Thanks Noha