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neherlab / treetime

Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
MIT License
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IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed #260

Open ritawyt opened 10 months ago

ritawyt commented 10 months ago

I'm running this code and run into an index error: treetime --tree /Users/ouotodou/Desktop/treeee.nex --dates /Users/ouotodou/Desktop/sampled_metadata.csv --aln /Users/ouotodou/Desktop/sampled_sequences.fasta

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

0.00 -TreeAnc: set-up

0.13 -WARNING: character 0 is unknown. Treating it as missing information

0.13 -WARNING: character 1 is unknown. Treating it as missing information Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/treetime.py", line 57, in run return self._run(**kwargs) ^^^^^^^^^^^^^^^^^^^ File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/treetime.py", line 215, in _run self.optimize_tree(infer_gtr=infer_gtr, File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/treeanc.py", line 1356, in optimize_tree self.optimize_branch_lengths_joint(store_old=False) File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/treeanc.py", line 1157, in optimize_branch_lengths_joint new_len = max(0,self.optimal_branch_length(node)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/treeanc.py", line 1202, in optimal_branch_length return self.gtr.optimal_t_compressed(node.branch_state['pair'], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/treetime/gtr.py", line 854, in optimal_t_compressed hamming_distance = np.sum(multiplicity[seq_pair[:,1]!=seq_pair[:,0]])/np.sum(multiplicity)


IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

ERROR: too many indices for array: array is 1-dimensional, but 2 were indexed 

ERROR in TreeTime.run: An error occurred which was not properly handled in TreeTime. If this error persists, please let us know by filing a new issue including the original command and the error above at: https://github.com/neherlab/treetime/issues 

Has anyone encountered this error before and knows how to solve it? Thank you so much!
ritawyt commented 10 months ago

I'm using binary data, so the sequences are consist of 0s and 1s

rneher commented 7 months ago

Hi @ritawyt, sorry about the slow reply. this is difficult to debug without being able to run the command. Is this data you can share?