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Error in mikado conda #451

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edugenetico opened this issue Apr 18, 2024 · 0 comments
Open

Error in mikado conda #451

edugenetico opened this issue Apr 18, 2024 · 0 comments

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@edugenetico
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Hello

I have installed mikado using the following steps on Ubuntu,

$ conda create -n mikado python==3.7.5
$ conda install -c anaconda gcc_linux-x64 gxx_linux-x64 zlib
$ pip install numpy scipy cython
$ export CONDA_BUILD=1 # instruct conda to use its own GCC/GXX while in this environment
$ pip install mikado==2.0rc2

And when running mikado --help I got the following error

/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/hsp.py:115: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.
Query.query_id == query_id))
/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/hsp.py:117: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.
Query.query_id == query_id))
/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/hit.py:71: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.
Query.query_id == query_id))
/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/hit.py:73: SAWarning: implicitly coercing SELECT object to scalar subquery; please use the .scalar_subquery() method to produce a scalar subquery.
Query.query_id == query_id))
Traceback (most recent call last):
File "/home/arolab/miniconda3/envs/mikado/bin/mikado", line 5, in
from Mikado import main
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/init.py", line 28, in
from . import configuration
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/configuration/init.py", line 7, in
from . import configurator
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/configuration/configurator.py", line 22, in
from ..transcripts.transcript import Transcript
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/transcripts/init.py", line 7, in
from .transcript import Transcript, Namespace
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/transcripts/transcript.py", line 26, in
from ..serializers.blast_serializer import Query, Hit
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/init.py", line 5, in
from . import blast_serializer
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/init.py", line 10, in
from .blast_serialiser import BlastSerializer
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/blast_serialiser.py", line 17, in
from .tab_serialiser import _serialise_tabular
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/tab_serialiser.py", line 1, in
from .tabular_utils import parse_tab_blast, get_queries, get_targets
File "/home/arolab/miniconda3/envs/mikado/lib/python3.7/site-packages/Mikado/serializers/blast_serializer/tabular_utils.py", line 1, in
from Bio.SubsMat import MatrixInfo
ModuleNotFoundError: No module named 'Bio.SubsMat'

Could you tell me how to fix it

Thanks

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