Closed ucassee closed 5 years ago
alneberg
commented
5 years ago That's weird. Did you install this using conda? It seems it is missing a gsl dependency. Can you specify the command you used and what packages that the conda environment include after the installation? Thanks!
ucassee
commented
5 years ago Hello @alneberg ,
I just use concoct -v to check the newly installed concoct. I install it using Anaconda follow the tutorial on your website. conda install cython numpy scipy biopython pandas pip scikit-learn
alneberg
commented
5 years ago Weird. Could you list the packages installed in your conda environment as listed by conda list? If that doesn't show anything strange I will attempt to reproduce this error.
ucassee
commented
5 years ago Hello @alneberg , The followings are packages installed in conda environment:
#
asn1crypto 0.24.0 py36_0
ca-certificates 2018.03.07 0
certifi 2018.8.24 py36_1
cffi 1.11.5 py36h9745a5d_0
chardet 3.0.4 py36h0f667ec_1
conda 4.5.11 py36_0
conda-env 2.6.0 h36134e3_1
cryptography 2.2.2 py36h14c3975_0
h5py 2.8.0
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 hdf63c60_3
libstdcxx-ng 7.2.0 hdf63c60_3
metabat2 2.12.1 0 ursky
ncurses 6.1 hf484d3e_0
numpy 1.15.4
pip 18.1
progressbar33 2.4
pycparser 2.18 py36hf9f622e_1
pyopenssl 18.0.0 py36_0
pysocks 1.6.8 py36_0
python 3.6.5 hc3d631a_2
python-dateutil 2.7.5
requests 2.18.4 py36he2e5f8d_1
ruamel_yaml 0.15.37 py36h14c3975_2
setuptools 39.2.0 py36_0
six 1.11.0 py36h372c433_1
sqlite 3.23.1 he433501_0
tk 8.6.7 hc745277_3
urllib3 1.22 py36hbe7ace6_0
wget 1.19.5 h1ad7b7a_0
wheel 0.31.1 py36_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 ha838bed_2
alneberg
commented
5 years ago That doesn't look like the concoct environment. You will have to have the environment activated when running the command. Sorry for being unclear.
ucassee
commented
5 years ago Hi @alneberg
#
biopython 1.68 py35_0 bioconda
blas 1.1 openblas conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
certifi 2018.8.24 py35_1001 conda-forge
concoct 1.0.0
alneberg
commented
5 years ago Ah, sorry. I now realise that the installation documentation is really lacking. This specific issue was solved in the conda recipe to install concoct from conda:
conda create -n concoct_env python=3 concoct
But using the commands present in the documentation will result in this error as you have discovered. Could you try and reinstall concoct with the above command? I will make an effort to update the documentation. Thanks!
ucassee
commented
5 years ago I find an interesting thing. If I use the root account, I can use the concoct without error. But I will try to reinstall it, because it is not available to normal user.
ucassee
commented
5 years ago I reinstall it. There is still an error.
(concoct_env) [zhouyl@localhost ~]$ concoct -v
Traceback (most recent call last):
File "/data2017/share/tools/miniconda3/envs/concoct_env/bin/concoct", line 4, in
the following is packages in new concoct_env: (concoct_env) [zhouyl@localhost ~]$ conda list
#
alabaster 0.7.12 py_0 conda-forge
asn1crypto 0.24.0 py35_3 conda-forge
babel 2.6.0 py_1 conda-forge
biopython 1.68 py35_0 bioconda
blas 1.1 openblas conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
certifi 2018.8.24 py35_1001 conda-forge
cffi 1.11.5 py35h5e8e0c9_1 conda-forge
chardet 3.0.4 py35_3 conda-forge
concoct 1.0.0 py35hd1ccf6d_1 bioconda
concoct 1.0.0
jinja2 2.10 py_1 conda-forge
jpeg 9c h14c3975_1001 conda-forge
krb5 1.16.3 hc83ff2d_1000 conda-forge
libcurl 7.64.0 h01ee5af_0 conda-forge
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 hf484d3e_1005 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libopenblas 0.3.3 h5a2b251_3
libpng 1.6.36 h84994c4_1000 conda-forge
libssh2 1.8.0 h1ad7b7a_1003 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge
libtiff 4.0.10 h648cc4a_1001 conda-forge
llvm-meta 7.0.0 0 conda-forge
markupsafe 1.0 py35h470a237_1 conda-forge
mkl 2019.1 144
mkl_fft 1.0.9 py35_0 conda-forge
mkl_random 1.0.1 py35_0 conda-forge
mmtf-python 1.0.2 py35_0 bioconda
msgpack-python 0.5.6 py35h2d50403_3 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
nose 1.3.7 py35_2 conda-forge
numpy 1.15.2 py35_blas_openblashd3ea46f_0 [blas_openblas] conda-forge
numpy-base 1.15.2 py35h2f8d375_0
olefile 0.46 py_0 conda-forge
openblas 0.2.20 8 conda-forge
openmp 7.0.0 h2d50403_0 conda-forge
openssl 1.0.2p h14c3975_1002 conda-forge
packaging 19.0 py_0 conda-forge
pandas 0.23.4 py35hf8a1672_0 conda-forge
pillow 5.3.0 py35hc736899_0 conda-forge
pip 18.0 py35_1001 conda-forge
pycparser 2.19 py_0 conda-forge
pygments 2.3.1 py_0 conda-forge
pyopenssl 18.0.0 py35_0 conda-forge
pyparsing 2.3.1 py_0 conda-forge
pysocks 1.6.8 py35_2 conda-forge
python 3.5.5 h5001a0f_2 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
reportlab 3.5.8 py35h77bcf2c_0 conda-forge
requests 2.19.1 py35_1 conda-forge
samtools 1.9 h57cc563_6 bioconda
scikit-learn 0.20.0 py35_blas_openblasha84fab4_201 [blas_openblas] conda-forge
scipy 1.1.0 py35_blas_openblash7943236_201 [blas_openblas] conda-forge
setuptools 40.4.3 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
snowballstemmer 1.2.1 py_1 conda-forge
sphinx 1.8.1 py35_0 conda-forge
sphinx_rtd_theme 0.4.3 py_0 conda-forge
sphinxcontrib-websupport 1.1.0 py_1 conda-forge
sqlite 3.26.0 h67949de_1000 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
urllib3 1.23 py35_1 conda-forge
wheel 0.32.0 py35_1000 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
alneberg
commented
5 years ago Well now it seems like you have two concoct installed in parallel. If you create a new environment and only run the conda command (and not any setup.py command) it should work.
ucassee
commented
5 years ago Hi @alneberg ，
It is work now. Thank you very much. Could you please help me to solve the input file problem you mentioned before. It also occurs in the new concoct version.
Up and running. Check /dataNew/User/zhouyl/sediment/metaWRAP/B11/log.txt for progress /data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:82: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. cov = p.read_table(cov_file, header=0, index_col=0) Traceback (most recent call last): File "/data2017/share/tools/miniconda3/envs/concoct_env/bin/concoct", line 88, in <module> results = main(args) File "/data2017/share/tools/miniconda3/envs/concoct_env/bin/concoct", line 40, in main args.seed File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.6/site-packages/concoct/transform.py", line 5, in perform_pca pca_object = PCA(n_components=nc, random_state=seed).fit(d) File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.6/site-packages/sklearn/decomposition/pca.py", line 340, in fit self._fit(X) File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.6/site-packages/sklearn/decomposition/pca.py", line 381, in _fit copy=self.copy) File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.6/site-packages/sklearn/utils/validation.py", line 582, in check_array context)) ValueError: Found array with 0 sample(s) (shape=(0, 139)) while a minimum of 1 is required.
alneberg
commented
5 years ago That's great!
Yes, I think it is caused by a mismatch of the lefthand column of the coverage table and the contig ids in the fasta file. Could you give me the first five contig names of the fasta file and see if these are also listed in the coverage file?
ucassee
commented
5 years ago the first five lines in coverage file are: 1 18.1576 2.85688 2 11.9123 7.08195 3 11.8578 7.6306 4 12.3037 7.30384 5 11.8619 7.26513
The first five contig names of the fasta file is
1 >2 >3 >4 >5
alneberg
commented
5 years ago Ah, it might be an old bug, where concoct doesn't allow contig ids to be only integers. Would that explain it?
ucassee
commented
5 years ago It is work after I replaced the contig ids. Thanks for your help~
alneberg
commented
5 years ago Ah, that's a relief! Good luck with your binning!
Hello developer, I install the the latest version of concoct(1.0.0), but there is an error to use it. Best regards Traceback (most recent call last): File "/data2017/share/tools/miniconda3/envs/concoct_env/bin/concoct", line 4, in
import('pkg_resources').run_script('concoct==1.0.0', 'concoct')
File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.5/site-packages/pkg_resources/init.py", line 661, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.5/site-packages/pkg_resources/init.py", line 1441, in run_script
exec(code, namespace, namespace)
File "/data2017/share/tools/miniconda3/envs/concoct_env/lib/python3.5/site-packages/concoct-1.0.0-py3.5-linux-x86_64.egg/EGG-INFO/scripts/concoct", line 6, in
import vbgmm
ImportError: libgsl.so.23: cannot open shared object file: No such file or directory