Concoct endless warning due to OpenBLAS

[HouyuZhang]

Dear ursky,
Thank you for developing this pipeline. I installed following your "Manual installation" suggestions and ran each module smoothly until the --concoct parameter in metawrap binning command, where I met endless warnings OpenBLAS Warning: Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
I have checked through each page on the internet related to this issue:

1. Have gone through GitHub endless OpenBLAS Warning BinPro/CONCOCT#232, I got a sense that the OpenMP and OpenBLAS module has problems. I saw your resolution for this is conda install -y blas=2.5=mkl, however, I cannot install this by the configuration you recommended in README. Instead, I ran conda install -y blas=*=*mkl but still did not solve the warning.
2. endless OpenBLAS Warning again BinPro/CONCOCT#316. Following this, I installed the concoct in a new environment using py3, instead of py2 as you recommended, but still did not work.
3. Request: Please create version with make USE_OPENMP=1  conda-forge/openblas-feedstock#79. Following this, I tried to install OpenBLAS and openMP against in conda by conda install libopenblas=*=*openmp* --channel conda-forge, not work.
4. Lastly, I used -t 1 to give up parallel running, but also did not work.

Do you have further suggestions on this issue? Also, it will help if you tell me an approximation of the running time of concoct.
Thanks in advance!

Houyu

[HouyuZhang]

Below is my conda env:
name: metawrap-env
channels:

• intel
• bioconda/label/cf201901
• conda-forge
• ursky
• bioconda
• defaults
  dependencies:
• _libgcc_mutex=0.1=conda_forge
• _openmp_mutex=4.5=2_kmp_llvm
• biopython=1.81=py310h1fa729e_0
• blas=2.106=mkl
• bowtie2=2.5.1=py310ha0a81b8_2
• brotli=1.0.9=h166bdaf_9
• brotli-bin=1.0.9=h166bdaf_9
• brotli-python=1.0.9=py310hd8f1fbe_9
• bwa=0.7.17=he4a0461_11
• bzip2=1.0.8=h7f98852_4
• c-ares=1.19.1=hd590300_0
• ca-certificates=2023.7.22=hbcca054_0
• certifi=2023.7.22=pyhd8ed1ab_0
• charset-normalizer=3.2.0=pyhd8ed1ab_0
• checkm-genome=1.2.2=pyhdfd78af_1
• concoct=1.1.0=py310h74abf4b_3
• contourpy=1.1.0=py310hd41b1e2_0
• cycler=0.11.0=pyhd8ed1ab_0
• cython=3.0.0=py310hc6cd4ac_0
• dendropy=4.6.1=pyhdfd78af_0
• fonttools=4.42.1=py310h2372a71_0
• fraggenescan=1.31=h031d066_6
• freetype=2.12.1=hca18f0e_1
• gettext=0.21.1=h27087fc_0
• gsl=2.7=he838d99_0
• hmmer=3.3.2=hdbdd923_4
• htslib=1.17=h81da01d_2
• icu=72.1=hcb278e6_0
• idba=1.1.3=1
• idna=3.4=pyhd8ed1ab_0
• intel-openmp=2023.1.0=hdb19cb5_46305
• jellyfish=1.1.12=h2d50403_0
• joblib=1.3.0=pyhd8ed1ab_1
• keyutils=1.6.1=h166bdaf_0
• kiwisolver=1.4.4=py310hbf28c38_1
• kraken=1.1=h470a237_2
• krb5=1.21.1=h659d440_0
• krona=2.7=0
• lcms2=2.15=haa2dc70_1
• ld_impl_linux-64=2.40=h41732ed_0
• lerc=4.0.0=h27087fc_0
• libblas=3.9.0=6_mkl
• libbrotlicommon=1.0.9=h166bdaf_9
• libbrotlidec=1.0.9=h166bdaf_9
• libbrotlienc=1.0.9=h166bdaf_9
• libcblas=3.9.0=6_mkl
• libcurl=8.2.0=hca28451_0
• libdeflate=1.18=h0b41bf4_0
• libedit=3.1.20191231=he28a2e2_2
• libev=4.33=h516909a_1
• libffi=3.4.2=h7f98852_5
• libgcc=7.2.0=h69d50b8_2
• libgcc-ng=13.1.0=he5830b7_0
• libgfortran-ng=13.1.0=h69a702a_0
• libgfortran5=13.1.0=h15d22d2_0
• libgomp=13.1.0=he5830b7_0
• libhwloc=2.9.1=nocuda_h7313eea_6
• libiconv=1.17=h166bdaf_0
• libidn2=2.3.4=h166bdaf_0
• libjpeg-turbo=2.1.5.1=h0b41bf4_0
• liblapack=3.9.0=6_mkl
• liblapacke=3.9.0=6_mkl
• libnghttp2=1.52.0=h61bc06f_0
• libnsl=2.0.0=h7f98852_0
• libopenblas=0.3.23=openmp_h2a4e791_0
• libpng=1.6.39=h753d276_0
• libsqlite=3.42.0=h2797004_0
• libssh2=1.11.0=h0841786_0
• libstdcxx-ng=13.1.0=hfd8a6a1_0
• libtiff=4.5.1=h8b53f26_0
• libunistring=0.9.10=h7f98852_0
• libuuid=2.38.1=h0b41bf4_0
• libwebp-base=1.3.1=hd590300_0
• libxcb=1.15=h0b41bf4_0
• libxml2=2.11.4=h0d562d8_0
• libzlib=1.2.13=hd590300_5
• llvm-openmp=16.0.6=h4dfa4b3_0
• matplotlib-base=3.7.1=py310he60537e_0
• maxbin2=2.2.1=0
• metabat2=2.12.1=0
• mkl=2020.4=h726a3e6_304
• mpi=1.0=openmpi
• munkres=1.0.7=py_1
• ncurses=6.4=hcb278e6_0
• nose=1.3.7=py_1006
• numpy=1.25.1=py310ha4c1d20_0
• openblas=0.3.23=openmp_hef934df_0
• openjpeg=2.5.0=hfec8fc6_2
• openmpi=4.1.5=h414af15_101
• openssl=3.1.2=hd590300_0
• packaging=23.1=pyhd8ed1ab_0
• pandas=2.0.3=py310h7cbd5c2_1
• perl=5.32.1=4_hd590300_perl5
• perl-threaded=5.22.0=13
• pillow=10.0.0=py310h582fbeb_0
• pip=23.2.1=pyhd8ed1ab_0
• platformdirs=3.9.1=pyhd8ed1ab_0
• pooch=1.7.0=pyha770c72_3
• pplacer=1.1.alpha19=h9ee0642_2
• prodigal=2.6.3=h031d066_6
• pthread-stubs=0.4=h36c2ea0_1001
• pyparsing=3.1.1=pyhd8ed1ab_0
• pysam=0.21.0=py310h41dec4a_1
• pysocks=1.7.1=pyha2e5f31_6
• python=3.10.12=hd12c33a_0_cpython
• python-dateutil=2.8.2=pyhd8ed1ab_0
• python-tzdata=2023.3=pyhd8ed1ab_0
• python_abi=3.10=3_cp310
• pytz=2023.3=pyhd8ed1ab_0
• readline=8.2=h8228510_1
• rename=1.601=hdfd78af_1
• requests=2.31.0=pyhd8ed1ab_0
• samtools=1.17=hd87286a_1
• scikit-learn=1.2.2=py310hf7d194e_2
• scipy=1.11.1=py310ha4c1d20_0
• setuptools=68.0.0=pyhd8ed1ab_0
• six=1.16.0=pyh6c4a22f_0
• spades=3.13.0=0
• sqlite=3.42.0=h2c6b66d_0
• tbb=2021.9.0=hf52228f_0
• threadpoolctl=3.2.0=pyha21a80b_0
• tk=8.6.12=h27826a3_0
• typing-extensions=4.7.1=hd8ed1ab_0
• typing_extensions=4.7.1=pyha770c72_0
• tzdata=2023c=h71feb2d_0
• unicodedata2=15.0.0=py310h5764c6d_0
• urllib3=2.0.4=pyhd8ed1ab_0
• wget=1.20.3=ha35d2d1_1
• wheel=0.41.0=pyhd8ed1ab_0
• xorg-libxau=1.0.11=hd590300_0
• xorg-libxdmcp=1.1.3=h7f98852_0
• xz=5.2.6=h166bdaf_0
• zlib=1.2.13=hd590300_5
• zstd=1.5.2=hfc55251_7
  prefix: /lustre/home/tangmoran_2021phd/anaconda3/envs/metawrap-env

[yqy6611]

Don't use that personal channel. Release python restrictions and install dependencies directly.