Problem with installation by conda

[bioinformatist]

Dear, I've noticed that the software came to v1.0.0, and it supports python 3.X now. So I just tried conda install concoct and everything looked well durining installation. However, when I tried command concoct, it throwed an error:

Traceback (most recent call last):
  File "/share/home/lzhiwei/.conda/envs/ysun-env/bin/concoct", line 6, in <module>
    import vbgmm
ImportError: /share/home/lzhiwei/.conda/envs/ysun-env/lib/python3.6/site-packages/vbgmm.cpython-36m-x86_64-linux-gnu.so: undefined symbol: Py_InitModule

It seems like a problem caused by library vbgmm. I try install it by pip or conda, but both of them say no proper version here. The python version is v3.6.7 in the virtual env. Can you help me?

[alneberg]

Yes, unfortunately the conda package is still not ready to be merged, you can keep track of the progress here: https://github.com/bioconda/bioconda-recipes/pull/12600

At least to begin with, macosx will not be supported, so if you are running a mac, you might need to do a specific install still. Please let me know if you need further assistance with that.

[bioinformatist]

Wow, what a quick reply! I'm using x86-64 Linux on HPC (you know, I'm not the one so conda makes things easier), and I'll keep concern with this recipe. Once it finished I would like try again with 3.x python and give you a response. Thanks for attention for this problem~

[alneberg]

@bioinformatist, the PR has now been merged and it should be possible to install the new version via conda on python 3 on Linux:

conda install concoct samtools

I forgot to add samtools as a dependency in the first conda recipe so it has to be installed additionally for now.

[bioinformatist]

Ahhhhh, thank you! The software by conda install with Linux and py3 works well now. And it seems samtools is already satisfied up to now~ Concoct is one of best binning softwares 😆

[alneberg]

Very pleased to hear! Just remember to set the -t flag to get the proper performance.

[ReneKat]

Hi @alneberg: I'm over here now. :) I have the latest versions of concoct and samtools installed and am getting the same error above:

packages in environment at /Users/Owl/miniconda3/envs/concoct_env:

#

Name Version Build Channel

alabaster 0.7.12 py_0 conda-forge babel 2.7.0 py_0 conda-forge biopython 1.74 py36h0b31af3_0 conda-forge bzip2 1.0.8 h01d97ff_1 conda-forge ca-certificates 2019.9.11 hecc5488_0 conda-forge certifi 2019.9.11 py36_0 conda-forge cffi 1.13.2 py36h33e799b_0 conda-forge chardet 3.0.4 py36_1003 conda-forge concoct 0.4.1 py36hd1ccf6d_0 bioconda cryptography 2.8 py36hafa8578_0 conda-forge curl 7.65.3 h22ea746_0 conda-forge cython 0.29.14 py36h4a8c4bd_0 conda-forge docutils 0.15.2 py36_0 conda-forge gsl 2.2.1 h002c638_3
htslib 1.9 h3a161e8_7 bioconda idna 2.8 py36_1000 conda-forge imagesize 1.1.0 py_0 conda-forge jinja2 2.10.3 py_0 conda-forge joblib 0.14.0 py_0 conda-forge krb5 1.16.3 hcfa6398_1001 conda-forge libblas 3.8.0 11_openblas conda-forge libcblas 3.8.0 11_openblas conda-forge libcurl 7.65.3 h16faf7d_0 conda-forge libcxx 9.0.0 h89e68fa_1 conda-forge libdeflate 1.0 h1de35cc_1 bioconda libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 1 bioconda libgfortran 3.0.1 0 conda-forge liblapack 3.8.0 11_openblas conda-forge libopenblas 0.3.6 hdc02c5d_2
libssh2 1.8.2 hcdc9a53_2 conda-forge llvm-openmp 9.0.0 h40edb58_0 conda-forge markupsafe 1.1.1 py36h0b31af3_0 conda-forge ncurses 6.1 h0a44026_1002 conda-forge nose 1.3.7 py36_1003 conda-forge numpy 1.17.3 py36hde6bac1_0 conda-forge openblas 0.2.20 8 conda-forge openssl 1.1.1d h0b31af3_0 conda-forge packaging 19.2 py_0 conda-forge pandas 0.25.3 py36h4f17bb1_0 conda-forge pip 19.3.1 py36_0 conda-forge pycparser 2.19 py36_1 conda-forge pygments 2.4.2 py_0 conda-forge pyopenssl 19.0.0 py36_0 conda-forge pyparsing 2.4.5 py_0 conda-forge pysocks 1.7.1 py36_0 conda-forge python 3.6.7 h4285619_1006 conda-forge python-dateutil 2.8.1 py_0 conda-forge pytz 2019.3 py_0 conda-forge readline 8.0 hcfe32e1_0 conda-forge requests 2.22.0 py36_1 conda-forge samtools 1.9 h8aa4d43_12 bioconda scikit-learn 0.21.3 py36hd4ffd6c_0 conda-forge scipy 1.3.1 py36hab3da7d_2 conda-forge setuptools 41.6.0 py36_1 conda-forge six 1.13.0 py36_0 conda-forge snowballstemmer 2.0.0 py_0 conda-forge sphinx 2.2.1 py_0 conda-forge sphinx_rtd_theme 0.4.3 py_0 conda-forge sphinxcontrib-applehelp 1.0.1 py_0 conda-forge sphinxcontrib-devhelp 1.0.1 py_0 conda-forge sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.2 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.3 py_0 conda-forge sqlite 3.30.1 h93121df_0 conda-forge tk 8.6.9 h2573ce8_1003 conda-forge urllib3 1.25.7 py36_0 conda-forge wheel 0.33.6 py36_0 conda-forge xz 5.2.4 h1de35cc_1001 conda-forge zlib 1.2.11 h0b31af3_1006 conda-forge

concoct --composition_file cSMMC_contigs_10K.fa --coverage_file cSMMC_coverage_table.tsv -b concoct_output/

Traceback (most recent call last): File "/Users/Owl/miniconda3/envs/concoct_env/bin/concoct", line 6, in import vbgmm ImportError: dlopen(/Users/Owl/miniconda3/envs/concoct_env/lib/python3.6/site-packages/vbgmm.cpython-36m-darwin.so, 2): Symbol not found: _Py_InitModule Referenced from: /Users/Owl/miniconda3/envs/concoct_env/lib/python3.6/site-packages/vbgmm.cpython-36m-darwin.so Expected in: flat namespace in /Users/Owl/miniconda3/envs/concoct_env/lib/python3.6/site-packages/vbgmm.cpython-36m-darwin.so

[alneberg]

Hi @ReneKat,

I can see in your list of packages that you're using concoct 0.4.1. Can you consider to upgrade to the latest version instead?

Thank you, Johannes

[ReneKat]

Hello Johannes (@alneberg), I can see from the change log that you're on version 1.1.0! So, yes my version is quite behind. However, when I run conda update concoct I get:

All requested packages already installed.

When I run: concoct -v I get the above error again.

I have only ever installed packages using conda. I'm running MacOS 10.14.6.

[alneberg]

There are some issues with the concoct conda build recipe where it is quite specific with some dependencies. I think the easiest way is to make completely new environment. Just follow the installations instructions again: https://concoct.readthedocs.io/en/latest/installation.html

It should be fairly quick. If you have something else in your current environment you can always switch between the two different environments (as long as you give them different names).

[mant-ux]

@bioinformatist Hello！I have the same problem as you after install it by Bioconda.

I have follow our author run conda install concoct samtools ,But it still reported an error. How did you run it successfully? Can you give me some help? I'm confused with vbgmm, Thank you very much.