I am currently using tensorflow==2.2 and keras==2.4.3 with Janggu in conda environment supplied below. My environment runs smoothly until I apply a Bidirectional LSTM keras layer. This outputs a an error NotImplementedError: Cannot convert a symbolic Tensor (bidirectional/forward_lstm/strided_slice:0) to a numpy array.
I then downgrade my numpy installation from 1.21 to 1.19.5 which then results in conflicts with keras.
The error that results is:
ValueError:validation_splitis only supported for Tensors or NumPy arrays, found: ([Bioseq("dna"), ReduceDim(Cover('rna')), ReduceDim(Cover('H3K4me3'))], ReduceDim(Cover('cage')), None)
Do you have any recommendations on how to resolve these issues. I cannot utilise tensorflow==1.14 and keras==2.2 due to hpc limitations.
Thank you so much!!
`# packages in environment at /share/anaconda3/envs/janggu:
#
I am currently using tensorflow==2.2 and keras==2.4.3 with Janggu in conda environment supplied below. My environment runs smoothly until I apply a Bidirectional LSTM keras layer. This outputs a an error
NotImplementedError: Cannot convert a symbolic Tensor (bidirectional/forward_lstm/strided_slice:0) to a numpy array.I then downgrade my numpy installation from 1.21 to 1.19.5 which then results in conflicts with keras. The error that results is:
ValueError:validation_splitis only supported for Tensors or NumPy arrays, found: ([Bioseq("dna"), ReduceDim(Cover('rna')), ReduceDim(Cover('H3K4me3'))], ReduceDim(Cover('cage')), None)Do you have any recommendations on how to resolve these issues. I cannot utilise tensorflow==1.14 and keras==2.2 due to hpc limitations.
Thank you so much!!
`# packages in environment at /share/anaconda3/envs/janggu: #
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge absl-py 1.0.0 pypi_0 pypi astunparse 1.6.3 pypi_0 pypi atk 2.36.0 ha770c72_4 conda-forge atk-1.0 2.36.0 h516909a_2 conda-forge bedtools 2.30.0 h468198e_3 bioconda biopython 1.77 py37h8f50634_1 conda-forge bottleneck 1.3.4 py37hda87dfa_1 conda-forge brotli 1.0.9 h166bdaf_7 conda-forge brotli-bin 1.0.9 h166bdaf_7 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge ca-certificates 2021.10.8 ha878542_0 conda-forge cachetools 4.2.4 pypi_0 pypi cairo 1.16.0 h18b612c_1001 conda-forge certifi 2021.10.8 py37h89c1867_2 conda-forge charset-normalizer 2.0.12 pypi_0 pypi curl 7.64.0 h646f8bb_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dbus 1.13.6 he372182_0 conda-forge expat 2.4.8 h27087fc_0 conda-forge fontconfig 2.14.0 h8e229c2_0 conda-forge fonttools 4.32.0 py37h540881e_0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gast 0.3.3 pypi_0 pypi gdk-pixbuf 2.38.2 h3f25603_4 conda-forge gettext 0.19.8.1 hf34092f_1004 conda-forge glib 2.66.1 h680cd38_0 conda-forge gobject-introspection 1.66.1 py37h619baee_1 conda-forge google-auth 1.35.0 pypi_0 pypi google-auth-oauthlib 0.4.6 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 2.42.3 h0511662_0 conda-forge grpcio 1.44.0 pypi_0 pypi gstreamer 1.14.5 h36ae1b5_2 conda-forge gtk2 2.24.32 h90f3771_0 conda-forge h5py 2.10.0 nompi_py37h513d04c_102 conda-forge harfbuzz 2.4.0 h37c48d4_1 conda-forge hdf5 1.10.5 nompi_h5b725eb_1114 conda-forge icu 58.2 hf484d3e_1000 conda-forge idna 3.3 pypi_0 pypi importlib-metadata 4.11.3 pypi_0 pypi janggu 0.10.2 pypi_0 pypi joblib 1.1.0 pyhd8ed1ab_0 conda-forge jpeg 9e h166bdaf_1 conda-forge keras 2.4.3 pypi_0 pypi keras-preprocessing 1.1.2 pypi_0 pypi kiwisolver 1.4.2 py37h7cecad7_1 conda-forge krb5 1.16.3 hc83ff2d_1000 conda-forge lcms2 2.12 hddcbb42_0 conda-forge libblas 3.9.0 14_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_7 conda-forge libbrotlidec 1.0.9 h166bdaf_7 conda-forge libbrotlienc 1.0.9 h166bdaf_7 conda-forge libcblas 3.9.0 14_linux64_openblas conda-forge libcurl 7.64.0 h01ee5af_0 conda-forge libdeflate 1.6 h516909a_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 11.2.0 h1d223b6_15 conda-forge libgfortran-ng 11.2.0 h69a702a_15 conda-forge libgfortran5 11.2.0 h5c6108e_15 conda-forge libgomp 11.2.0 h1d223b6_15 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 14_linux64_openblas conda-forge libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge libpng 1.6.37 h21135ba_2 conda-forge libssh2 1.8.0 h1ad7b7a_1003 conda-forge libstdcxx-ng 11.2.0 he4da1e4_15 conda-forge libtiff 4.2.0 hf544144_3 conda-forge libtool 2.4.6 h9c3ff4c_1008 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.2 h7f98852_1 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.9.9 h13577e0_2 conda-forge libzlib 1.2.11 h166bdaf_1014 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge markdown 3.3.6 pypi_0 pypi matplotlib 3.5.1 py37h89c1867_0 conda-forge matplotlib-base 3.5.1 py37h1058ff1_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge numexpr 2.8.0 py37h85a3170_102 conda-forge numpy 1.21.6 py37h976b520_0 conda-forge oauthlib 3.2.0 pypi_0 pypi olefile 0.46 pyh9f0ad1d_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openssl 1.0.2u h516909a_0 conda-forge opt-einsum 3.3.0 pypi_0 pypi packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.3.5 py37h8c16a72_0 pango 1.42.4 h7062337_4 conda-forge patsy 0.5.2 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pillow 8.2.0 py37h4600e1f_1 conda-forge pip 22.0.4 pyhd8ed1ab_0 conda-forge pixman 0.38.0 h516909a_1003 conda-forge progress 1.6 pyhd8ed1ab_0 conda-forge protobuf 3.20.0 pypi_0 pypi pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyasn1 0.4.8 pypi_0 pypi pyasn1-modules 0.2.8 pypi_0 pypi pybedtools 0.9.0 py37h595c7a6_1 bioconda pybigwig 0.3.13 py37h5295baf_2 bioconda pydot 1.4.2 py37h89c1867_1 conda-forge pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge pyqt 5.6.0 py37h13b7fb3_1008 conda-forge pysam 0.15.4 pypi_0 pypi python 3.7.0 hd21baee_1006 conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.7 2_cp37m conda-forge pytz 2022.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0 pypi_0 pypi qt 5.6.2 hce4f676_1013 conda-forge readline 7.0 hf8c457e_1001 conda-forge requests 2.27.1 pypi_0 pypi requests-oauthlib 1.3.1 pypi_0 pypi rsa 4.8 pypi_0 pypi scikit-learn 1.0.2 py37hf9e9bfc_0 conda-forge scipy 1.4.1 pypi_0 pypi seaborn 0.11.2 hd8ed1ab_0 conda-forge seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge setuptools 62.1.0 py37h89c1867_0 conda-forge sip 4.18.1 py37hf484d3e_1000 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sqlite 3.28.0 h8b20d00_0 conda-forge statsmodels 0.13.2 py37hb1e94ed_0 conda-forge tensorboard 2.2.2 pypi_0 pypi tensorboard-plugin-wit 1.8.1 pypi_0 pypi tensorflow 2.2.0 pypi_0 pypi tensorflow-estimator 2.2.0 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tornado 6.1 py37h540881e_3 conda-forge typing-extensions 4.2.0 hd8ed1ab_0 conda-forge typing_extensions 4.2.0 pyha770c72_0 conda-forge unicodedata2 14.0.0 py37h540881e_1 conda-forge urllib3 1.26.9 pypi_0 pypi werkzeug 2.1.1 pypi_0 pypi wheel 0.37.1 pyhd8ed1ab_0 conda-forge wrapt 1.14.0 pypi_0 pypi xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxpm 3.5.13 h7f98852_0 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge zipp 3.8.0 pypi_0 pypi zlib 1.2.11 h166bdaf_1014 conda-forge zstd 1.5.2 ha95c52a_0 conda-forge`