apcamargo
commented
3 months ago Hi @WUD2018,
Thank you for your report. It seems like this is the same bug reported by @erinyoung here. The problem is that Keras 3 created some incompatibilities which leads to a few problems in geNomad. In the future I'll investigate updating the code to support Keras 3, but for the time being I restricted to keras <3.0.
I just pushed version 1.7.6 which should fix this. You can fix in your own environment by downgrading Keras.
WUD2018
Hey developer,
Thanks for your efforts to develop this tool.
I have successfully installed the genomad via mamba:
mamba create -n genomad -c conda-forge -c bioconda genomad
and
genomad download-database .
However, when the pipelines run to 'Encoding' sequences: an issue jumps out as below. Could you please help me out?
......
[00:53:25] geNomad marker-classification finished!
╭──────────────────────────────────────────────────────────────────────────────╮ │ Executing geNomad nn-classification (v1.7.5). This will classify the input │ │ sequences into chromosome, plasmid, or virus based on the nucleotide │ │ sequence. │ │ ────────────────────────────────────────────────────────────────────────── │ │ Outputs: │ │ genomad_output/AnimFece_bin.1_nn_classification │ │ ├── AnimFece_bin.1_nn_classification.json (execution parameters) │ │ ├── AnimFece_bin.1_encoded_sequences (directory containing encoded │ │ │ sequence data) │ │ ├── AnimFece_bin.1_nn_classification.tsv (contig classification: tabular │ │ │ format) │ │ └── AnimFece_bin.1_nn_classification.npz (contig classification: binary │ │ format) │ ╰──────────────────────────────────────────────────────────────────────────────╯ [00:53:27] Executing genomad nn-classification.
[00:53:27] Creating the genomad_output/AnimFece_bin.1_nn_classification
directory.
[00:53:27] Creating the
genomad_output/AnimFece_bin.1_nn_classification/AnimFece_bin.1_encode d_sequences directory.
[00:53:28] Encoded sequence data written to AnimFece_bin.1_encoded_sequences.
Traceback (most recent call last): File "/home/dell/anaconda3/envs/genomad/bin/genomad", line 10, in
sys.exit(cli())
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(args, kwargs)
File "/home/dell/.local/lib/python3.10/site-packages/rich_click/rich_command.py", line 126, in main
rv = self.invoke(ctx)
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(args, kwargs)
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, *kwargs)
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/cli.py", line 1276, in end_to_end
ctx.invoke(
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(args, kwargs)
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/cli.py", line 719, in nn_classification
genomad.nn_classification.main(
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/modules/nn_classification.py", line 309, in main
nn_model = neural_network.create_classifier()
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/neural_network/model.py", line 34, in create_classifier
encoder = create_encoder()
File "/home/dell/anaconda3/envs/genomad/lib/python3.10/site-packages/genomad/neural_network/model.py", line 14, in create_encoder
inputs = Input(shape=5_997, dtype="int64")
File "/home/dell/.local/lib/python3.10/site-packages/keras/src/layers/core/input_layer.py", line 143, in Input
layer = InputLayer(
File "/home/dell/.local/lib/python3.10/site-packages/keras/src/layers/core/input_layer.py", line 46, in init
shape = backend.standardize_shape(shape)
File "/home/dell/.local/lib/python3.10/site-packages/keras/src/backend/common/variables.py", line 442, in standardize_shape
raise ValueError(f"Cannot convert '{shape}' to a shape.")
ValueError: Cannot convert '5997' to a shape.
Here is my conda list of genomad env:
packages in environment at /home/dell/anaconda3/envs/genomad:
#
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _py-xgboost-mutex 2.0 cpu_0 conda-forge absl-py 2.1.0 pyhd8ed1ab_0 conda-forge aiohttp 3.9.3 py310h2372a71_1 conda-forge aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge aragorn 1.2.41 h031d066_1 bioconda archspec 0.2.3 pyhd8ed1ab_0 conda-forge aria2 1.37.0 h347180d_1 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-timeout 4.0.3 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge blinker 1.7.0 pyhd8ed1ab_0 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.27.0 hd590300_0 conda-forge ca-certificates 2024.2.2 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.3 pyhd8ed1ab_0 conda-forge certifi 2024.2.2 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cryptography 42.0.5 py310h75e40e8_0 conda-forge flatbuffers 23.5.26 h59595ed_1 conda-forge frozenlist 1.4.1 py310h2372a71_0 conda-forge gast 0.5.4 pyhd8ed1ab_0 conda-forge gawk 5.3.0 ha916aea_0 conda-forge genomad 1.7.5 pyhdfd78af_0 bioconda gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h0b41bf4_3 conda-forge gmp 6.3.0 h59595ed_1 conda-forge google-auth 2.28.2 pyhca7485f_0 conda-forge google-auth-oauthlib 1.2.0 pyhd8ed1ab_0 conda-forge google-pasta 0.2.0 pyh8c360ce_0 conda-forge grpcio 1.59.3 py310h1b8f574_0 conda-forge h5py 3.10.0 nompi_py310h65828d5_101 conda-forge hdf5 1.14.3 nompi_h4f84152_100 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.6 pyhd8ed1ab_0 conda-forge importlib-metadata 7.0.2 pyha770c72_0 conda-forge joblib 1.3.2 pyhd8ed1ab_0 conda-forge keras 2.15.0 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge libabseil 20230802.1 cxx17_h59595ed_0 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libblas 3.9.0 21_linux64_openblas conda-forge libcblas 3.9.0 21_linux64_openblas conda-forge libcurl 8.6.0 hca28451_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_5 conda-forge libgfortran-ng 13.2.0 h69a702a_5 conda-forge libgfortran5 13.2.0 ha4646dd_5 conda-forge libgomp 13.2.0 h807b86a_5 conda-forge libgrpc 1.59.3 hd6c4280_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.7 hd590300_0 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 21_linux64_openblas conda-forge libllvm14 14.0.6 hcd5def8_4 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge libpng 1.6.43 h2797004_0 conda-forge libprotobuf 4.24.4 hf27288f_0 conda-forge libre2-11 2023.09.01 h7a70373_1 conda-forge libsqlite 3.45.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxgboost 2.0.3 cpu_h6728c87_1 conda-forge libxml2 2.12.6 h232c23b_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge llvmlite 0.42.0 py310h1b8f574_1 conda-forge markdown 3.6 pyhd8ed1ab_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.5 py310h2372a71_0 conda-forge mdurl 0.1.2 pyhd8ed1ab_0 conda-forge ml_dtypes 0.2.0 py310hcc13569_2 conda-forge mmseqs2 14.7e284 pl5321h6a68c12_2 bioconda mpfr 4.2.1 h9458935_0 conda-forge multidict 6.0.5 py310h2372a71_0 conda-forge ncurses 6.4 h59595ed_2 conda-forge numba 0.59.0 py310h7dc5dd1_1 conda-forge numpy 1.26.4 py310hb13e2d6_0 conda-forge oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge openssl 3.2.1 hd590300_1 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge protobuf 4.24.4 py310h620c231_0 conda-forge py-xgboost 2.0.3 cpu_pyh0a621ce_1 conda-forge pyasn1 0.5.1 pyhd8ed1ab_0 conda-forge pyasn1-modules 0.3.0 pyhd8ed1ab_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.17.2 pyhd8ed1ab_0 conda-forge pyjwt 2.8.0 pyhd8ed1ab_1 conda-forge pyopenssl 24.0.0 pyhd8ed1ab_0 conda-forge pyrodigal 3.3.0 py310h4b81fae_1 bioconda pyrodigal-gv 0.3.1 pyh7cba7a3_0 bioconda pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.10.13 hd12c33a_1_cpython conda-forge python-crfsuite 0.9.9 py310hd41b1e2_2 conda-forge python-flatbuffers 24.3.7 pyh59ac667_0 conda-forge python_abi 3.10 4_cp310 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge re2 2023.09.01 h7f4b329_1 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.31.0 pyhd8ed1ab_0 conda-forge requests-oauthlib 1.4.0 pyhd8ed1ab_0 conda-forge rich 13.7.1 pyhd8ed1ab_0 conda-forge rich-click 1.7.4 pyhd8ed1ab_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge scikit-learn 1.4.1.post1 py310h1fdf081_0 conda-forge scipy 1.12.0 py310hb13e2d6_2 conda-forge setuptools 69.2.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge taxopy 0.12.0 pyhdfd78af_0 bioconda tensorboard 2.15.2 pyhd8ed1ab_0 conda-forge tensorboard-data-server 0.7.0 py310h75e40e8_1 conda-forge tensorflow 2.15.0 cpu_py310h7825f03_2 conda-forge tensorflow-base 2.15.0 cpu_py310h7e4d085_2 conda-forge tensorflow-estimator 2.15.0 cpu_py310haacee6a_2 conda-forge termcolor 2.4.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.3.0 pyhc1e730c_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge typing-extensions 4.10.0 hd8ed1ab_0 conda-forge typing_extensions 4.10.0 pyha770c72_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge urllib3 2.2.1 pyhd8ed1ab_0 conda-forge werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge wget 1.21.4 hda4d442_0 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge wrapt 1.14.1 py310h5764c6d_1 conda-forge xgboost 2.0.3 cpu_pyhb06c54e_1 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yarl 1.9.4 py310h2372a71_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge