isaacovercast
commented
6 months ago You might check the toytree version installed? There was an update to v3.0 recently which broke some things. Try rolling back to toytree 2.0.5 and let me know how it goes.
On Thu, May 30, 2024, 20:15 DavidRJB @.***> wrote:
Hello!
I was wondering if I can get some help with the error. I followed all the recommendations in ipyrad page and the input data its from ipyrad too.
data = "/mnt/netapp1/Store_csbepgnf/seqs/tetrad/c90m131d6/c90m131d6_outs.snps.hdf5"
tet = ipa.tetrad( name="virentes-min4", data=data, nquartets=1e6, nboots=16, )
loading snps array [265 taxa x 45801 snps] max unlinked SNPs per quartet [nloci]: 1597 quartet sampler [random]: 1000000 / 200860990
tet.run(auto=True) Traceback (most recent call last): File "", line 1, in File "/mnt/netapp1/Store_csbepgnf/mambaforge/envs/tetrad_env/lib/python3.7/site-packages/tetrad/tetrad.py", line 527, in run self._get_checkpoint() File "/mnt/netapp1/Store_csbepgnf/mambaforge/envs/tetrad_env/lib/python3.7/site-packages/tetrad/tetrad.py", line 217, in _get_checkpoint self._finished_full = toytree.tree(self.trees.tree).ntips > 1 File "/mnt/netapp1/Store_csbepgnf/mambaforge/envs/tetrad_env/lib/python3.7/site-packages/toytree/io/src/treeio.py", line 82, in tree internal_labels=internal_labels, File "/mnt/netapp1/Store_csbepgnf/mambaforge/envs/tetrad_env/lib/python3.7/site-packages/toytree/io/src/parse.py", line 116, in parse_tree strdata = parse_generic_to_str(data) File "/mnt/netapp1/Store_csbepgnf/mambaforge/envs/tetrad_env/lib/python3.7/site-packages/toytree/io/src/parse.py", line 74, in parse_generic_to_str "Tree input appears to be a file path " OSError: Tree input appears to be a file path but does not exist: '/mnt/netapp1/Store_csbepgnf/seqs/tetrad/c90m131d6/analysis-tetrad/virentes-min4.tree'
I checked the analysis-tetrad and only appeared virentes-min4.input.hdf5 file. I received other error message but it was solved (AttributeError: 'str' object has no attribute 'decode')
Thanks!
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alexkrohn
Hello!
I was wondering if I can get some help with the error. I followed all the recommendations in ipyrad page and the input data its from ipyrad too.
loading snps array [265 taxa x 45801 snps] max unlinked SNPs per quartet [nloci]: 1597 quartet sampler [random]: 1000000 / 200860990
I checked the analysis-tetrad and only appeared virentes-min4.input.hdf5 file. I received other error message but it was solved (AttributeError: 'str' object has no attribute 'decode')
Thanks!