Installing deepBGC
planctoqueen opened this issue · 8 comments
I am trying to install deepBGC on my pc but I'm havig some issues that I cannot solve.
I am using Python3.7.0 and conda and already added all the necessary channels. However, everytime I try to install deepBGC I get this issue:
I already try with and without forcing the deepBGC version and get the same error everytime.
Can you please help?
Thanks!~
Hi @planctoqueen can you share the full error output and also the output of conda info ?
Hi @prihoda ,
thanks for the wquick answer.
This is the full error output
And here the conda info:
Thank you!
Hmm, not sure what could be wrong honestly. I hope this is not a broader issue. Anyway, you should be able to install the dependencies from conda manually and then install deepbgc using pip:
conda install prodigal hmmer
pip install deepbgcIs there an update on this? I'm having a similar issue and looks like the same error when trying 'conda install deepbgc' with and without the '-c conda-forge' flag
the solution proposed by @prihoda on May 18th 'looks' like it worked, but when i try to do the first cmd on the tutorial 'deepbgc download' i get the following:
(deepbgc) PS A:\Akshar> conda install prodigal hmmer
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- prodigal
- hmmer
Current channels:
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/win-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
(deepbgc) PS A:\Akshar> deepbgc download
| _ \ ___ ___ ____ | __ ) / ) / )
| | \ / _ / _ \ _ | _ \ | | _ | |
| |/ / __/ __/ |) | |) || || || |_
|/ _|_| /|/ _| ___)
=================||===== version 0.1.29 =====
INFO 05/10 14:11:46 Creating download directory: C:\Users\TRaveler\AppData\Local\deepbgc\deepbgc\data\0.1.0
INFO 05/10 14:11:46 ================================================================================
INFO 05/10 14:11:46 Checking: C:\Users\TRaveler\AppData\Local\deepbgc\deepbgc\data\0.1.0\detector\deepbgc.pkl
INFO 05/10 14:11:46 Downloading: https://github.com/Merck/deepbgc/releases/download/v0.1.0/deepbgc.pkl
ERROR 05/10 14:11:46 0
Traceback (most recent call last):
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\main.py", line 113, in main
run(argv)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\main.py", line 102, in run
args.func.run(**args_dict)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\command\download.py", line 25, in run
util.download_files(DOWNLOADS)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\util.py", line 403, in download_files
download_file(url=url, target_path=target_path, checksum=checksum, gzipped=gzipped)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\util.py", line 425, in download_file
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 525, in open
response = self._open(req, data)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 543, in _open
'_open', req)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 503, in _call_chain
result = func(*args)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 1393, in https_open
context=self._context, check_hostname=self._check_hostname)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 1318, in do_open
h = http_class(host, timeout=req.timeout, **http_conn_args)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\http\client.py", line 1416, in init
context = ssl._create_default_https_context()
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 589, in create_default_context
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 490, in load_default_certs
self._load_windows_store_certs(storename, purpose)
File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 482, in _load_windows_store_certs
self.load_verify_locations(cadata=certs)
ssl.SSLError: unknown error (_ssl.c:4034)
ERROR 05/10 14:11:46 ================================================================================
ERROR 05/10 14:11:46 DeepBGC failed with SSLError
ERROR 05/10 14:11:46 ================================================================================
ERROR 05/10 14:11:46 unknown error (_ssl.c:4034)
Also, I don't think hmmer or prodigal have actually been installed..
Hey @alohith this looks like a network issue, can you try creating a separate environment and paste the log here?
conda create -n deepbgc python=3.7
conda activate deepbgc
conda install deepbgcHi @prihoda here's what it looks like. Very similar to what I was seeing before, also the same if I instead say 'python=3.6'
(base) PS A:\Akshar> conda create -n deepbgc python=3.7
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: C:\Users\TRaveler\.conda\envs\deepbgc
added / updated specs:
- python=3.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2021.5.30 | h5b45459_0 171 KB conda-forge
openssl-3.0.0 | h8ffe710_1 10.0 MB conda-forge
pip-21.2.4 | pyhd8ed1ab_0 1.1 MB conda-forge
python-3.7.10 |h900ac77_102_cpython 17.9 MB conda-forge
python_abi-3.7 | 2_cp37m 4 KB conda-forge
setuptools-58.2.0 | py37h03978a9_0 1.0 MB conda-forge
sqlite-3.36.0 | h8ffe710_2 1.2 MB conda-forge
ucrt-10.0.20348.0 | h57928b3_0 1.2 MB conda-forge
vc-14.2 | hb210afc_5 13 KB conda-forge
vs2015_runtime-14.29.30037 | h902a5da_5 1.3 MB conda-forge
wheel-0.37.0 | pyhd8ed1ab_1 31 KB conda-forge
------------------------------------------------------------
Total: 33.9 MB
The following NEW packages will be INSTALLED:
ca-certificates conda-forge/win-64::ca-certificates-2021.5.30-h5b45459_0
openssl conda-forge/win-64::openssl-3.0.0-h8ffe710_1
pip conda-forge/noarch::pip-21.2.4-pyhd8ed1ab_0
python conda-forge/win-64::python-3.7.10-h900ac77_102_cpython
python_abi conda-forge/win-64::python_abi-3.7-2_cp37m
setuptools conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
sqlite conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
ucrt conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
vc conda-forge/win-64::vc-14.2-hb210afc_5
vs2015_runtime conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
wheel conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1
Proceed ([y]/n)? y
Downloading and Extracting Packages
python_abi-3.7 | 4 KB | ############################################################################ | 100%
ucrt-10.0.20348.0 | 1.2 MB | ############################################################################ | 100%
openssl-3.0.0 | 10.0 MB | ############################################################################ | 100%
python-3.7.10 | 17.9 MB | ############################################################################ | 100%
sqlite-3.36.0 | 1.2 MB | ############################################################################ | 100%
ca-certificates-2021 | 171 KB | ############################################################################ | 100%
pip-21.2.4 | 1.1 MB | ############################################################################ | 100%
wheel-0.37.0 | 31 KB | ############################################################################ | 100%
vc-14.2 | 13 KB | ############################################################################ | 100%
setuptools-58.2.0 | 1.0 MB | ############################################################################ | 100%
vs2015_runtime-14.29 | 1.3 MB | ############################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate deepbgc
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) PS A:\Akshar> conda activate deepbgc
(deepbgc) PS A:\Akshar> conda install deepbgc
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: -
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
(deepbgc) PS A:\Akshar>
Hi!
I don't know if this is the correct solution but what solve the problem for me was to remove the conda-forge channel. conda config --remove channels conda-forge
hope it helps!~
I have tried to run commands in anaconda powershell with conda create -n deepbgc python=3.7 hmmer prodigal, conda activate deepbgc and pip install deepbgc and seems hmmer and prodigal have been successfully downloaded . I have attached the output of following commands.
conda create -n deepbgc python=3.7 hmmer prodigal output:
pip install deepbgc output:
end...:
However, every time I run the command conda install deepbgc, it keep showing me this issue:
Btw, this is the info of my conda:
Could somebody help me to solve the issue, your help would greatly appreciated for me. Thank you.