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oschwengers
DeepSig could not be executed! Please make sure DeepSig is installed and executable
Hello, I've installed Bakta using Conda with Python 3.8. Deepsig has been installed but I still have the Deepsig error:
> bakta --db /home/bakta/db --genus klebsiella --gram - --threads 8 -v --o genome_238_bakta genome_238.fasta
> ERROR: DeepSig could not be executed! Please make sure DeepSig is installed and executable or skip requiring workflow steps via via '--gram ?'.
Packages installed in the conda environment are:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_tflow_select 2.3.0 mkl
about-time 4.2.1 pyhd8ed1ab_0 conda-forge
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
alive-progress 3.0.1 pyhd8ed1ab_0 conda-forge
aragorn 1.2.41 h031d066_1 bioconda
archspec 0.2.2 pyhd8ed1ab_0 conda-forge
astor 0.8.1 pyh9f0ad1d_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
bakta 1.9.2 pyhdfd78af_0 bioconda
biopython 1.78 py38h7f8727e_0 anaconda
blast 2.14.0 h7d5a4b4_1 bioconda
brotli-python 1.0.9 py38h6a678d5_7 anaconda
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.21.0 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py38h5eee18b_0 anaconda
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
circos 0.69.9 hdfd78af_0 bioconda
curl 8.4.0 hca28451_0 conda-forge
deepsig 1.2.5 pyhdfd78af_0 bioconda
diamond 2.1.8 h43eeafb_0 bioconda
entrez-direct 16.2 he881be0_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gast 0.3.3 py_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
grapheme 0.6.0 pyhd8ed1ab_0 conda-forge
grpcio 1.59.3 py38h94a1851_0 conda-forge
h5py 2.10.0 nompi_py38h513d04c_102 conda-forge
hdf5 1.10.5 nompi_h5b725eb_1114 conda-forge
hmmer 3.3.2 hdbdd923_4 bioconda
icu 73.2 h59595ed_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
infernal 1.1.4 pl5321h031d066_4 bioconda
isa-l 2.30.0 hd590300_6 conda-forge
keras 2.4.3 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 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
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20230802.1 cxx17_h59595ed_0 conda-forge
libblas 3.9.0 19_linux64_openblas conda-forge
libcblas 3.9.0 19_linux64_openblas conda-forge
libcurl 8.4.0 hca28451_0 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_2 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgfortran-ng 13.2.0 h69a702a_2 conda-forge
libgfortran5 13.2.0 ha4646dd_2 conda-forge
libgomp 13.2.0 h807b86a_2 conda-forge
libgrpc 1.59.3 hd6c4280_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 19_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.24 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 3.44.0 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_2 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp 1.3.2 h658648e_1 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
markdown 3.5.2 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py38h01eb140_0 conda-forge
ncbi-amrfinderplus 3.11.26 h283d18e_0 bioconda
ncurses 6.4 h59595ed_2 conda-forge
numpy 1.24.4 py38h59b608b_0 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
opt_einsum 3.3.0 pyhc1e730c_2 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 4_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-b-cow 0.007 pl5321h166bdaf_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-clone 0.46 pl5321h166bdaf_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge
perl-config-general 2.65 pl5321hdfd78af_0 bioconda
perl-digest-perl-md5 1.9 pl5321hdfd78af_2 bioconda
perl-encode 3.19 pl5321h166bdaf_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-config 0.008 pl5321ha770c72_0 conda-forge
perl-extutils-helpers 0.026 pl5321ha770c72_0 conda-forge
perl-extutils-installpaths 0.012 pl5321ha770c72_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-extutils-pl2bat 0.005 pl5321ha770c72_0 conda-forge
perl-font-ttf 1.06 pl5321hdfd78af_1 bioconda
perl-gd 2.76 pl5321h5b5514e_1 bioconda
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-compress 2.201 pl5321hdbdd923_2 bioconda
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h4ac6f70_6 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h031d066_2 bioconda
perl-math-bezier 0.01 pl5321hdfd78af_2 bioconda
perl-math-round 0.07 pl5321ha770c72_0 conda-forge
perl-math-vecstat 0.08 pl5321hdfd78af_2 bioconda
perl-module-build 0.4232 pl5321ha770c72_0 conda-forge
perl-module-build-tiny 0.039 pl5321h166bdaf_0 conda-forge
perl-module-implementation 0.09 pl5321ha770c72_0 conda-forge
perl-module-runtime 0.016 pl5321ha770c72_0 conda-forge
perl-number-format 1.76 pl5321hdfd78af_0 bioconda
perl-params-validate 1.31 pl5321hec16e2b_0 bioconda
perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h166bdaf_0 conda-forge
perl-readonly 2.05 pl5321ha770c72_0 conda-forge
perl-regexp-common 2017060201 pl5321hd8ed1ab_0 conda-forge
perl-scalar-list-utils 1.63 pl5321h166bdaf_0 conda-forge
perl-set-intspan 1.19 pl5321hdfd78af_2 bioconda
perl-statistics-basic 1.6611 pl5321hdfd78af_3 bioconda
perl-storable 3.15 pl5321h166bdaf_0 conda-forge
perl-svg 2.87 pl5321hd8ed1ab_0 conda-forge
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
perl-text-format 0.62 pl5321hdfd78af_0 bioconda
perl-time-hires 1.9764 pl5321h031d066_4 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-xml-parser 2.44_01 pl5321hc3e0081_1003 conda-forge
pigz 2.8 h2797004_0 conda-forge
piler-cr 1.06 h4ac6f70_4 bioconda
pip 23.3.1 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
pooch 1.8.1 pyhd8ed1ab_0 conda-forge
protobuf 4.24.4 py38hf14ab21_0 conda-forge
psutil 5.9.0 py38h5eee18b_0 anaconda
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyhmmer 0.10.6 py38he5da3d1_0 bioconda
pyrodigal 3.3.0 py38he5da3d1_0 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.18 hd12c33a_0_cpython conda-forge
python-isal 1.6.0 py38h01eb140_0 conda-forge
python_abi 3.8 4_cp38 conda-forge
pyyaml 6.0.1 py38h5eee18b_0 anaconda
re2 2023.06.02 h2873b5e_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
scipy 1.10.1 py38h59b608b_3 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
tensorboard 2.16.2 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.7.0 py38hcdda232_1 conda-forge
tensorflow 2.2.0 mkl_py38h6d3daf0_0
tensorflow-base 2.2.0 mkl_py38h5059a2d_0
tensorflow-estimator 2.6.0 py38h709712a_0 conda-forge
termcolor 2.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
trnascan-se 2.0.12 pl5321h031d066_0 bioconda
tzdata 2023c h71feb2d_0 conda-forge
urllib3 2.0.7 pyhd8ed1ab_0 conda-forge
werkzeug 3.0.1 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
wheel 0.41.3 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py38h01eb140_0 conda-forge
xopen 1.9.0 py38h578d9bd_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstandard 0.19.0 py38h5eee18b_0 anaconda
zstd 1.5.5 hfc55251_0 conda-forge
Any idea how I can fix this please?
Hi @daisy238, this is interesting. Can you check if you can manually execute DeepSig within the activated environment?
If this is the case, could you then please execute Bakta with the --debug flag set and provide the log file so that I can take a deeper look into this?
Hi Oli, I have the same issue. Installed bakta with mamba and installed deepsig with pip (in the environment). bakta still gives an error that deepsig is not found. "ERROR: DeepSig could not be executed! Please make sure DeepSig is installed and executable or skip requiring workflow steps via via '--gram ?'."
Any ideas how to fix it?
update1: I also have a bakta 1.9.1 environment (with mamba) and checked if this is working, same Error with deepsig. In this environment I am not able to run deepsig without further installation of it.
update2: I installed a clean environment with bakta1.8.2 this morning and the same error occurs.
update3 with solution: I created a new blank environment and installed first deepsig with mamba and than bakta, now it works fine.
Hey Michael, thanks for the report. I guess this is not a bug in Bakta, but actually a simple dependency conflict in Mamba. DeepSig has several dependencies to pinned old Python (3.8) and Tensorflow packages. This is the reason, why I explicitly excluded DeepSig from the Bakta environment as this would hold back important updates.
As you've shown that it is actually working, we can exclude that this is a general issue in Bakta. Hence, I'll close this issue. I'll add a clear statement for others after closing this. Thanks again and best regards!
As @MiSchwabe pointed out, this is not a bug in Bakta, but a conflict with DeepSig's Python/Tensorflow dependency versions and other Bakta dependencies.
The solution is:
- Create a lean fresh environment
- Install DeepSig
- Install Bakta