SyntaxError: invalid syntax

[tuttigiuperterra]

I've installed source tracker with Conda. Then I run this command:

sourcetracker2 gibbs -i metagenome_OTU.txt -m map.txt -o output/

I did receive this error message and no output:

Traceback (most recent call last): File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/bin/sourcetracker2", line 6, in from sourcetracker._cli import cli File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/init.py", line 19, in import_module('sourcetracker._cli.gibbs') File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_cli/gibbs.py", line 23, in from sourcetracker._sourcetracker import ( File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/sourcetracker/_sourcetracker.py", line 15, in from skbio.stats import subsample_counts File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/init.py", line 13, in import skbio.io # noqa File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/init.py", line 238, in import_module('skbio.io.format.lsmat') File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/io/format/lsmat.py", line 77, in from skbio.stats.distance import DissimilarityMatrix, DistanceMatrix File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/init.py", line 192, in from ._base import (DissimilarityMatrixError, DistanceMatrixError, File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 13, in from IPython.core.pylabtools import print_figure File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/init.py", line 55, in from .terminal.embed import embed File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/embed.py", line 16, in from IPython.terminal.interactiveshell import TerminalInteractiveShell File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/IPython/terminal/interactiveshell.py", line 18, in from prompt_toolkit.enums import DEFAULT_BUFFER, EditingMode File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/init.py", line 16, in from .application import Application File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/application/init.py", line 1, in from .application import Application File "/Users/bioinfo/opt/anaconda3/envs/sourcetracker2/lib/python3.5/site-packages/prompt_toolkit/application/application.py", line 255 self.full_screen: bool = full_screen ^ SyntaxError: invalid syntax

What should I do?

[vfonti]

I've just had the same error message. Have you managed to solve it?

[vfonti]

I've just realized I had got an error message because of cython, which I had not installed. If you fixed that, it should work.