I have trying to run sourcetracker 2 with the following command:
source activate st2
sourcetracker2 -i Lean_d14d70.otu.txt -m Lean_d14d70.meta.txt -o Leandonor_14_70 --per_sink_feature_assignments --jobs=16
I am getting the following error message every time:
Traceback (most recent call last):
File "/panfs/roc/groups/8/cmstaley/mhkhan/.local/bin/sourcetracker2", line 5, in
from sourcetracker._cli.gibbs import gibbs
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/sourcetracker/init.py", line 11, in
from ._sourcetracker import gibbs
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 17, in
from skbio.stats import subsample_counts
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/init.py", line 11, in
import skbio.io # noqa
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/io/init.py", line 243, in
import_module('skbio.io.format.clustal')
File "/panfs/roc/msisoft/anaconda/python3-2020.07-mamba/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/io/format/clustal.py", line 148, in
from skbio.alignment import TabularMSA
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/alignment/init.py", line 204, in
from ._pairwise import (
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/alignment/_pairwise.py", line 15, in
from skbio.alignment._ssw_wrapper import StripedSmithWaterman
File "skbio/alignment/_ssw_wrapper.pyx", line 1, in init skbio.alignment._ssw_wrapper
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject
--------------------x---------------------------------------x--------------------------------------------x---------------------------------x
Now, I have uninstalling the conda and re-installing it by both ways i.e., with and without developmental version but it gave me the same error. I have checked my files and they seems fine. I don't what the issue is. Kindly help.
I have trying to run sourcetracker 2 with the following command: source activate st2 sourcetracker2 -i Lean_d14d70.otu.txt -m Lean_d14d70.meta.txt -o Leandonor_14_70 --per_sink_feature_assignments --jobs=16
I am getting the following error message every time:
Traceback (most recent call last): File "/panfs/roc/groups/8/cmstaley/mhkhan/.local/bin/sourcetracker2", line 5, in
from sourcetracker._cli.gibbs import gibbs
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/sourcetracker/init.py", line 11, in
from ._sourcetracker import gibbs
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/sourcetracker/_sourcetracker.py", line 17, in
from skbio.stats import subsample_counts
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/init.py", line 11, in
import skbio.io # noqa
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/io/init.py", line 243, in
import_module('skbio.io.format.clustal')
File "/panfs/roc/msisoft/anaconda/python3-2020.07-mamba/lib/python3.8/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/io/format/clustal.py", line 148, in
from skbio.alignment import TabularMSA
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/alignment/init.py", line 204, in
from ._pairwise import (
File "/home/cmstaley/mhkhan/.local/lib/python3.8/site-packages/skbio/alignment/_pairwise.py", line 15, in
from skbio.alignment._ssw_wrapper import StripedSmithWaterman
File "skbio/alignment/_ssw_wrapper.pyx", line 1, in init skbio.alignment._ssw_wrapper
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 80 from PyObject
--------------------x---------------------------------------x--------------------------------------------x---------------------------------x
Now, I have uninstalling the conda and re-installing it by both ways i.e., with and without developmental version but it gave me the same error. I have checked my files and they seems fine. I don't what the issue is. Kindly help.