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TypeError: __init__() takes 2 positional arguments but 3 were given #24
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Dear @marcejuarez90 Thanks for using read2tree. I would suggest using python version 3.10.8 (with a fresh environment) instead of python 3.7. I also suggest running read2tree on the test dataset provided on the github page. You can run in two steps
If still you have an issue, please let us how you find the gene markers and the command you run. Best regards, |
Hello, I'm also experiencing a similar issue to the one posed in issue #24. I also have the error "TypeError: init() takes 2 positional arguments but 3 were given" and I'm still encountering problems. My python version is 3.10.8. I found the marker genes using the OMA browser and instructions from your GitHub. It could easy be my code because I'm an absolute beginner. The file attached explains how I selected the marker genes, and the code I ran for making the tree: I would be very grateful if you have any advice or can help. Kind regards, Alice |
Dear Alice @afairnie Thanks for reaching out. Could you please send us the
Could you please try the same procedure ?
As I didn't have your sequencing reads, I only run the first step of read2tree by adding I'm also wondering what is your Biopython version? mine is 1.81 Best, |
Hi, I'm trying to use read2tree, but after it finishes making the orthologous genes selection and allignment it gives me the error I'm attaching. I suspect that it has something to do with this specific line in the Aligner.py script:
SeqRecord(Seq("".join(self._get_translated_seq_list(codon, str(rec.seq))), generic_dna), id=rec.id))
the error is:
TypeError: init() takes 2 positional arguments but 3 were given
maybe I am doing something wrong. I've tried to use it both in single and multi species mode but it crashes in the same place.
Also I'm attaching the print out of the error. Could you help me please? and thanks a lot, it looks like a very promising tool
--- Load OGs with min 0 species from oma OMA/marker_genes - mode = marker_genes --- Loading files for pre-filter: 100%|████████████████████████████████████████████| 8047/8047 [00:00<00:00, 10035.98 OGs/s]2023-05-05 14:02:34,049
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, **kwds))
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(*args))
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 292, in _align_worker align.dna = self._get_translated_alignment(codons, alignment)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 218, in _get_translated_alignment
SeqRecord(Seq("".join(self._get_translated_seq_list(codon, str(rec.seq))), generic_dna), id=rec.id))
TypeError: init() takes 2 positional arguments but 3 were given """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/mjuarez/anaconda3/bin/read2tree", line 4, in import('pkg_resources').run_script('read2tree==0.1.5', 'read2tree')
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 667, in run_script self.require(requires)[0].run_script(script_name, ns)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1470, in run_script exec(script_code, namespace, namespace)
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/EGG-INFO/scripts/read2tree", line 16, in
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/main.py", line 291, in main
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 51, in init
File "/home/mjuarez/anaconda3/lib/python3.7/site-packages/read2tree-0.1.5-py3.7.egg/read2tree/Aligner.py", line 330, in _align File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/mjuarez/anaconda3/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value
TypeError: init() takes 2 positional arguments but 3 were given
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