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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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undefined symbol error in end-to-end pipeline #65

Open DOieGYuan opened 6 months ago

DOieGYuan commented 6 months ago

Hi. Dear developer. Thank you for making this awesome tool! I use Genomad to annotate metagenomic assemble (i.e., contigs) using the end-to-end pipeline. When the message "geNomad marker-classification finished!" shows up, I get the error message as follows, Traceback (most recent call last): File "/home/nature/anaconda3/envs/virus/bin/genomad", line 10, in sys.exit(cli()) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/rich_click/rich_command.py", line 126, in main rv = self.invoke(ctx) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, *kwargs) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/genomad/cli.py", line 1276, in end_to_end ctx.invoke( File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/genomad/cli.py", line 719, in nn_classification genomad.nn_classification.main( File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/genomad/modules/nn_classification.py", line 35, in main import tensorflow as tf File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/init.py", line 48, in from tensorflow._api.v2 import internal File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/_api/v2/internal/init.py", line 8, in from tensorflow._api.v2.internal import autograph File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/_api/v2/internal/autograph/init.py", line 8, in from tensorflow.python.autograph.core.ag_ctx import control_status_ctx # line: 34 File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/autograph/core/ag_ctx.py", line 21, in from tensorflow.python.autograph.utils import ag_logging File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/autograph/utils/init.py", line 17, in from tensorflow.python.autograph.utils.context_managers import control_dependency_on_returns File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/autograph/utils/context_managers.py", line 19, in from tensorflow.python.framework import ops File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/framework/ops.py", line 40, in from tensorflow.python import pywrap_tensorflow File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/pywrap_tensorflow.py", line 34, in self_check.preload_check() File "/home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/platform/self_check.py", line 63, in preload_check from tensorflow.python.platform import _pywrap_cpu_feature_guard ImportError: /home/nature/anaconda3/envs/virus/lib/python3.10/site-packages/tensorflow/python/platform/../../libtensorflow_framework.so.2: undefined symbol: _ZTIN6snappy4SinkE

Could you help me figure out what is the problem? Thank you so much.

Sincerely,

DOieGYuan

apcamargo commented 6 months ago

Hi @DOieGYuan

Can you check which version of TensorFlow and Keras you have installed?

DOieGYuan commented 6 months ago

Hi @DOieGYuan

Can you check which version of TensorFlow and Keri's you have installed?

Hi @apcamargo. Thank you for you reply. I follow the instructions to install Genomad using mamba in the user guide. The TensorFlow is v2.15.0. And I'm not sure whether Keri's is installed because I only see keras (v2.15.0) in the conda environment.

Follows are the results of conda list:

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 2.0.0 pyhd8ed1ab_0 conda-forge aiohttp 3.9.1 pypi_0 pypi aiosignal 1.3.1 pyhd8ed1ab_0 conda-forge aragorn 1.2.41 h031d066_1 bioconda archspec 0.2.2 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 pypi_0 pypi attrs 23.1.0 pypi_0 pypi blas 1.1 openblas conda-forge blinker 1.7.0 pyhd8ed1ab_0 conda-forge brotli 1.1.0 pypi_0 pypi brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.24.0 hd590300_0 conda-forge ca-certificates 2023.12.12 h06a4308_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.2 pyhd8ed1ab_0 conda-forge certifi 2023.11.17 pypi_0 pypi cffi 1.16.0 pypi_0 pypi charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 pypi_0 pypi cryptography 41.0.7 pypi_0 pypi flatbuffers 23.5.26 h59595ed_1 conda-forge frozenlist 1.4.1 pypi_0 pypi gast 0.5.4 pyhd8ed1ab_0 conda-forge gawk 5.3.0 ha916aea_0 conda-forge genomad 1.7.4 pyhdfd78af_0 bioconda gettext 0.21.1 h27087fc_0 conda-forge giflib 5.2.1 h5eee18b_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main gmp 6.3.0 h59595ed_0 conda-forge google-auth 2.25.2 pyhca7485f_0 conda-forge google-auth-oauthlib 1.2.0 pyhd8ed1ab_0 conda-forge google-pasta 0.2.0 pyhd3eb1b0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main grpcio 1.59.3 pypi_0 pypi h5py 3.10.0 pypi_0 pypi 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 7.0.1 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 libcurl 8.5.0 hca28451_0 conda-forge libedit 3.1.20230828 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main libev 4.33 hd590300_2 conda-forge libffi 3.4.4 h6a678d5_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libgrpc 1.59.3 hd6c4280_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 3.0.0 hd590300_1 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 0.3.25 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 4.24.4 hf27288f_0 conda-forge libre2-11 2023.06.02 h7a70373_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libunistring 0.9.10 h27cfd23_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxgboost 2.0.3 cpu_h6728c87_0 conda-forge libxml2 2.12.3 h232c23b_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge llvmlite 0.41.1 pypi_0 pypi markdown 3.5.1 pyhd8ed1ab_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.3 pypi_0 pypi mdurl 0.1.0 pypi_0 pypi ml-dtypes 0.2.0 pypi_0 pypi ml_dtypes 0.2.0 py310hcc13569_2 conda-forge mmseqs2 14.7e284 pl5321h6a68c12_2 bioconda mpfr 4.2.1 h9458935_0 conda-forge multidict 6.0.4 pypi_0 pypi ncurses 6.4 h59595ed_2 conda-forge numba 0.58.1 pypi_0 pypi numpy 1.26.2 pypi_0 pypi numpy-base 1.26.2 py310h8a23956_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main oauthlib 3.2.2 pypi_0 pypi openblas 0.3.25 pthreads_h7a3da1a_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge opt_einsum 3.3.0 pyhc1e730c_2 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge protobuf 4.24.4 pypi_0 pypi py-xgboost 2.0.3 cpu_py310h78d450f_0 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_0 conda-forge pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge pyrodigal 3.2.1 pypi_0 pypi pyrodigal-gv 0.3.1 pyh7cba7a3_0 bioconda pysocks 1.7.1 pypi_0 pypi python 3.10.13 hd12c33a_1_cpython conda-forge python-crfsuite 0.9.9 pypi_0 pypi python-flatbuffers 23.5.26 pyhd8ed1ab_0 conda-forge python_abi 3.10 4_cp310 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge re2 2023.06.02 h2873b5e_0 conda-forge readline 8.2 h8228510_1 conda-forge requests 2.31.0 pypi_0 pypi requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge rich 13.7.0 pyhd8ed1ab_0 conda-forge rich-click 1.7.2 pyhd8ed1ab_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge scikit-learn 1.3.2 pypi_0 pypi scipy 1.11.4 pypi_0 pypi setuptools 68.2.2 pypi_0 pypi six 1.16.0 pyhd3eb1b0_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main snappy 1.1.10 h6a678d5_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main taxopy 0.12.0 pyhdfd78af_0 bioconda tensorboard 2.15.1 pyhd8ed1ab_0 conda-forge tensorboard-data-server 0.7.0 pypi_0 pypi tensorflow 2.15.0 pypi_0 pypi tensorflow-base 2.15.0 cpu_py310h7e4d085_1 conda-forge tensorflow-estimator 2.15.0 pypi_0 pypi termcolor 2.3.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.2.0 pyha21a80b_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge typing_extensions 4.9.0 pyha770c72_0 conda-forge tzdata 2023d h0c530f3_0 conda-forge urllib3 1.26.18 pypi_0 pypi werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge wget 1.21.4 h251f7ec_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main wrapt 1.14.1 pypi_0 pypi xgboost 2.0.3 pypi_0 pypi xz 5.4.5 h5eee18b_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main yarl 1.9.3 pypi_0 pypi zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge

apcamargo commented 6 months ago

I meant Keras, that was a typo.

I couldn't reproduce the issue. Can you delete the environment and install everything again?

mamba remove --all -n genomad
mamba clean --all
DOieGYuan commented 6 months ago

I meant Keras, that was a typo.

I couldn't reproduce the issue. Can you delete the environment and install everything again?

mamba remove --all -n genomad
mamba clean --all

Hi apcamargo. I tried but encountered the same issue. The command I used was genomad end-to-end --cleanup --splits 4 test.fa genomad_test Genomad_db And the fasta file is test.zip

apcamargo commented 6 months ago

Thanks for providing the FASTA file.

I couldn't reproduce the bug, I tested different TensorFlow/Keras versions. Do you have a GPU in the computer you're trying to run geNomad on?