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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
41 stars 12 forks source link

Incompatible package versions #46

Open lewhiteside opened 1 year ago

lewhiteside commented 1 year ago

Hi Saskia, I have downloaded Decona with the following commands:


git clone --recurse-submodules https://github.com/Saskia-Oosterbroek/decona.git
cd decona
git submodule update --init
cd install
module load apps/anaconda3/2021.05/bin
./install.sh
conda activate decona

However when I run the following command:

decona -f -l 300 -m 8000 -q 10 -c 0.80 -n 100 -M -B SILVA_138.1_SSURef_tax_silva.fasta

I get the following error:


ImportError: this version of pandas is incompatible with numpy < 1.20.3
your numpy version is 1.19.2.
Please upgrade numpy to >= 1.20.3 to use this pandas version

Any help with this would be greatly appresciated,

conda list

gives:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_openmp_mutex             5.1                       1_gnu
_tflow_select             2.3.0                       mkl
absl-py                   1.3.0            py38h06a4308_0
aiohttp                   3.8.3            py38h5eee18b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py38h06a4308_0
astunparse                1.6.3                      py_0
async-timeout             4.0.2            py38h06a4308_0
attrs                     22.1.0           py38h06a4308_0
bcftools                  1.10.2               h4f4756c_3    bioconda
biopython                 1.78             py38h7f8727e_0
blas                      1.0                         mkl
blinker                   1.4              py38h06a4308_0
bottleneck                1.3.5            py38h7deecbd_0
brotlipy                  0.7.0           py38h27cfd23_1003
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.18.1               h7f8727e_0
ca-certificates           2022.10.11           h06a4308_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py38h06a4308_0
cffi                      1.15.1           py38h74dc2b5_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py38h06a4308_0
cryptography              38.0.1           py38h9ce1e76_0
deprecated                1.2.13           py38h06a4308_0
fftw                      3.3.9                h27cfd23_1
frozenlist                1.3.3            py38h5eee18b_0
gast                      0.4.0              pyhd3eb1b0_0
gdbm                      1.18                 hd4cb3f1_4
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.4              pyhd3eb1b0_0
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py38hce63b2e_0
gsl                       2.6                  ha341630_0
h5py                      2.10.0           py38hd6299e0_1
hdf5                      1.10.6               h3ffc7dd_1
htslib                    1.10.2               hd3b49d5_1    bioconda
idna                      3.4              py38h06a4308_0
importlib-metadata        4.11.3           py38h06a4308_0
intel-openmp              2021.4.0          h06a4308_3561
intervaltree              3.1.0              pyhd3eb1b0_0
isa-l                     2.30.0               ha770c72_4    conda-forge
k8                        0.2.5                h9a82719_1    bioconda
keras-preprocessing       1.1.2              pyhd3eb1b0_0
krb5                      1.19.2               hac12032_0
ld_impl_linux-64          2.38                 h1181459_1
libcurl                   7.86.0               h91b91d3_0
libdeflate                1.6                  h516909a_0    conda-forge
libedit                   3.1.20210714         h7f8727e_0
libev                     4.33                 h7f8727e_1
libffi                    3.3                  he6710b0_2
libgcc-ng                 11.2.0               h1234567_1
libgfortran-ng            11.2.0               h00389a5_1
libgfortran5              11.2.0               h1234567_1
libgomp                   11.2.0               h1234567_1
libiconv                  1.16                 h7f8727e_2
libnghttp2                1.46.0               hce63b2e_0
libprotobuf               3.20.1               h4ff587b_0
libssh2                   1.10.0               h8f2d780_0
libstdcxx-ng              11.2.0               h1234567_1
lz4-c                     1.9.4                h6a678d5_0
mappy                     2.22             py38h390ddb8_0    bioconda
markdown                  3.4.1            py38h06a4308_0
markupsafe                2.1.1            py38h7f8727e_0
medaka                    1.1.2            py38hfcf0ad1_0    bioconda
minimap2                  2.17                 h5bf99c6_4    bioconda
mkl                       2021.4.0           h06a4308_640
mkl-service               2.4.0            py38h7f8727e_0
mkl_fft                   1.3.1            py38hd3c417c_0
mkl_random                1.2.2            py38h51133e4_0
multidict                 6.0.2            py38h5eee18b_0
nanofilt                  2.7.1                      py_0    bioconda
nanoget                   1.18.1             pyhdfd78af_0    bioconda
nanomath                  1.2.1              pyhdfd78af_0    bioconda
ncurses                   6.2                  he6710b0_1
networkx                  2.8.4            py38h06a4308_0
numexpr                   2.8.4            py38he184ba9_0
numpy                     1.19.2           py38h7895c89_1
numpy-base                1.19.2           py38h4c65ebe_1
oauthlib                  3.2.1            py38h06a4308_0
ont-fast5-api             4.1.0              pyhdfd78af_0    bioconda
openssl                   1.1.1s               h7f8727e_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 21.3               pyhd3eb1b0_0
pandas                    1.5.2            py38h417a72b_0
parasail-python           1.2.4            py38h8e3bb3f_1    bioconda
pbzip2                    1.1.13                        0    conda-forge
perl                      5.34.0               h5eee18b_2
pigz                      2.6                  h27cfd23_0
pip                       22.3.1           py38h06a4308_0
progressbar33             2.4                        py_0    conda-forge
protobuf                  3.20.1           py38h295c915_0
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyfaidx                   0.7.1              pyh5e36f6f_0    bioconda
pyjwt                     2.4.0            py38h06a4308_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py38h06a4308_0
pysam                     0.16.0.1         py38hbdc2ae9_1    bioconda
pysocks                   1.7.1            py38h06a4308_0
pyspoa                    0.0.3            py38h8ded8fe_3    bioconda
python                    3.8.12               h12debd9_0
python-dateutil           2.8.2              pyhd3eb1b0_0
python-edlib              1.3.9            py38h4a32c8e_1    bioconda
python-flatbuffers        2.0                pyhd3eb1b0_0
python-isal               0.11.1           py38h497a2fe_1    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.1           py38h06a4308_0
pyvcf3                    1.0.3              pyhdfd78af_0    bioconda
pyyaml                    6.0              py38h5eee18b_1
qcat                      1.1.0              pyh864c0ab_1    bioconda
racon                     1.4.13               he513fc3_0    bioconda
readline                  8.1                  h27cfd23_0
requests                  2.28.1           py38h06a4308_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
samtools                  1.10                 h2e538c0_3    bioconda
scipy                     1.9.3            py38h14f4228_0
setuptools                65.5.0           py38h06a4308_0
six                       1.16.0             pyhd3eb1b0_1
sortedcontainers          2.4.0              pyhd3eb1b0_0
sqlite                    3.40.0               h5082296_0
tar                       1.34                 ha1f6473_0    conda-forge
tensorboard               2.10.0           py38h06a4308_0
tensorboard-data-server   0.6.1            py38h52d8a92_0
tensorboard-plugin-wit    1.8.1            py38h06a4308_0
tensorflow                2.4.1           mkl_py38hb2083e0_0
tensorflow-base           2.4.1           mkl_py38h43e0292_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
termcolor                 2.1.0            py38h06a4308_0
tk                        8.6.12               h1ccaba5_0
urllib3                   1.26.13          py38h06a4308_0
werkzeug                  2.2.2            py38h06a4308_0
whatshap                  1.1              py38h8c62d01_1    bioconda
wheel                     0.37.1             pyhd3eb1b0_0
wrapt                     1.14.1           py38h5eee18b_0
xopen                     1.5.0            py38h578d9bd_0    conda-forge
xz                        5.2.8                h5eee18b_0
yaml                      0.2.5                h7b6447c_0
yarl                      1.8.1            py38h5eee18b_0
zipp                      3.8.0            py38h06a4308_0
zlib                      1.2.13               h5eee18b_0
zstd                      1.5.2                ha4553b6_0
Robvh-git commented 9 months ago

you can upgrade numpy by running following line in the linux terminal:

pip install numpy --upgrade