import vbgmm

[Vicbuz]

Hello,

When I run concoct I get the following error:

import vbgmm ImportError: libgsl.so.25: cannot open shared object file: No such file or directory

The current fix I found is to enter my conda enviroment and install mkl:

conda install mkl

However this didn't solve my issue. Packages in my environment are:

Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
appdirs 1.4.4 pyhd3eb1b0_0
biopython 1.78 py310h7f8727e_0
blas 1.0 mkl
bottleneck 1.3.5 py310ha9d4c09_0
brotlipy 0.7.0 py310h7f8727e_1002
bzip2 1.0.8 h7b6447c_0
c-ares 1.19.0 h5eee18b_0
ca-certificates 2023.01.10 h06a4308_0
certifi 2023.5.7 py310h06a4308_0
cffi 1.15.1 py310h5eee18b_3
charset-normalizer 2.0.4 pyhd3eb1b0_0
concoct 1.1.0 py310h07c81ac_3 bioconda
cryptography 39.0.1 py310h9ce1e76_0
curl 7.88.1 h5eee18b_0
cython 0.29.33 py310h6a678d5_0
gsl 2.7.1 h6e86dc7_1
idna 3.4 py310h06a4308_0
intel-openmp 2023.1.0 hdb19cb5_46305
joblib 1.1.1 py310h06a4308_0
krb5 1.19.4 h568e23c_0
ld_impl_linux-64 2.38 h1181459_1
libcurl 7.88.1 h91b91d3_0
libedit 3.1.20221030 h5eee18b_0
libev 4.33 h7f8727e_1
libffi 3.4.4 h6a678d5_0
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libnghttp2 1.46.0 hce63b2e_0
libssh2 1.10.0 h8f2d780_0
libstdcxx-ng 11.2.0 h1234567_1
libuuid 1.41.5 h5eee18b_0
llvm-openmp 14.0.6 h9e868ea_0
mkl 2023.1.0 h6d00ec8_46342
mkl-service 2.4.0 py310h5eee18b_1
mkl_fft 1.3.6 py310h1128e8f_1
mkl_random 1.2.2 py310h1128e8f_1
mpi 1.0 mpich
mpich 4.1.1 hbae89fd_0
ncurses 6.4 h6a678d5_0
nose 1.3.7 pyhd3eb1b0_1008
numexpr 2.8.4 py310h85018f9_1
numpy 1.24.3 py310h5f9d8c6_1
numpy-base 1.24.3 py310hb5e798b_1
openssl 1.1.1t h7f8727e_0
packaging 23.0 py310h06a4308_0
pandas 1.5.3 py310h1128e8f_0
pip 23.0.1 py310h06a4308_0
pooch 1.4.0 pyhd3eb1b0_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 23.0.0 py310h06a4308_0
pysocks 1.7.1 py310h06a4308_0
python 3.10.11 h7a1cb2a_2
python-dateutil 2.8.2 pyhd3eb1b0_0
python_abi 3.10 2_cp310 conda-forge
pytz 2022.7 py310h06a4308_0
readline 8.2 h5eee18b_0
requests 2.29.0 py310h06a4308_0
samtools 1.6 hb116620_7 bioconda
scikit-learn 1.2.2 py310h6a678d5_0
scipy 1.10.1 py310h5f9d8c6_1
setuptools 66.0.0 py310h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.41.2 h5eee18b_0
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 2.2.0 pyh0d69192_0
tk 8.6.12 h1ccaba5_0
tzdata 2023c h04d1e81_0
urllib3 1.26.15 py310h06a4308_0
wheel 0.38.4 py310h06a4308_0
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h5eee18b_0

Additionally I checked it was being called from the right place:

`(concoct) $ which concoct

/mnt/shared/scratch/apps/conda/envs/concoct/bin/concoct`

Can anyone suggest another step? I installed using the conda recommended steps.

[Vicbuz]

I solved this by using a symlink to the shared libs in conda. Specifically, I searched for the library to check it existed:

find -name "libgsl.so.25"

./apps/conda/envs/picrust2/lib/libgsl.so.25
./apps/conda/envs/medaka/lib/libgsl.so.25
./apps/conda/envs/lefse/lib/libgsl.so.25
./apps/conda/envs/qiime2-2022.8/lib/libgsl.so.25
./apps/conda/pkgs/gsl-2.7-he838d99_0/lib/libgsl.so.25

Then used a symlink inside from the shared library to the concoct library, so that concoct could access it, like so:

ln -s /home/apps/conda/pkgs/gsl-2.7-he838d99_0/lib/libgsl.so.25 /home/apps/conda/envs/concoct/lib/libgsl.so.25

I hope this helps someone.

[99qaz]

Hello, may I ask if the issue 'No module named 'vbgmm'' has been resolved?