[BUG] Eggnog mapper not running in workflow, works fine manually in same conda env

[timternetnet]

Short description of the problem

I'm trying to include Eggnog mapper in an Anvio workflow, but it stops with a non descriptive error. No clue if it's an issue with my workflow of with my installation.

anvi'o version

anvi-self-test --version
Anvi'o .......................................: marie (v8)
Python .......................................: 3.10.13

Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

Ubuntu 22.04

Installation:

Follow https://anvio.org/install/linux/stable/ (conda install)

anvi-setup-scg-taxonomy --scgs-taxonomy-data-dir /Taxonomy/802/anvio-8 -T 20 --reset
anvi-setup-ncbi-cogs --cog-data-dir  /Taxonomy/802/anvio-8 -T 20
anvi-setup-kegg-data --kegg-data-dir /Taxonomy/802/anvio-8/KEGG -T 20

conda install pulp=2.7.0

conda install -c bioconda krakenuniq
root@bw25c802:/Taxonomy/802/krakenuniq# krakenuniq-download --db DB --taxa "archaea,bacteria,viral,fungi,protozoa" --dust --exclude-environmental-taxa microbial-nt --threads 32
krakenuniq-build --db DB --kmer-len 31 --threads 30 --taxids-for-genomes --taxids-for-sequences --jellyfish-bin $(type -P -a jellyfish) --jellyfish-hash-size 30000000000

conda install -c bioconda -c conda-forge eggnog-mapper
download_eggnog_data.py --data_dir /Taxonomy/802/anvio-8-eggnogmapper

conda install bioconda::metabat2

Result:

conda list -n anvio-8
# packages in environment at /usr/local/bin/miniconda3/envs/anvio-8:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
_sysroot_linux-64_curr_repodata_hack 3                   h69a702a_14    conda-forge
amply                     0.1.6              pyhd8ed1ab_0    conda-forge
anvio                     8                        pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
archspec                  0.2.2              pyhd8ed1ab_0    conda-forge
asgiref                   3.7.2                    pypi_0    pypi
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     23.2.0                   pypi_0    pypi
binutils_impl_linux-64    2.40                 hf600244_0    conda-forge
bioconductor-qvalue       2.34.0            r43hdfd78af_0    bioconda
biopython                 1.83            py310h2372a71_0    conda-forge
blast                     2.14.1          pl5321h6f7f691_0    bioconda
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
bottle                    0.12.25                  pypi_0    pypi
bowtie2                   2.5.3           py310ha0a81b8_0    bioconda
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bwa                       0.7.17              he4a0461_11    bioconda
bwidget                   1.9.16               h9eba36c_0
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.26.0               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cairo                     1.16.0            hbbf8b49_1016    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
coin-or-cbc               2.10.10              h9002f0b_0    conda-forge
coin-or-cgl               0.60.7               h516709c_0    conda-forge
coin-or-clp               1.17.8               h1ee7a9c_0    conda-forge
coin-or-osi               0.108.8              ha2443b9_0    conda-forge
coin-or-utils             2.11.9               hee58242_0    conda-forge
coincbc                   2.10.10           0_metapackage    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
colored                   2.2.4                    pypi_0    pypi
conda                     23.11.0         py310hff52083_1    conda-forge
conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
configargparse            1.7                      pypi_0    pypi
connection-pool           0.0.3                    pypi_0    pypi
contourpy                 1.2.0                    pypi_0    pypi
curl                      8.5.0                hca28451_0    conda-forge
cycler                    0.12.1                   pypi_0    pypi
datrie                    0.8.2                    pypi_0    pypi
diamond                   2.1.8                h43eeafb_0    bioconda
dill                      0.3.8                    pypi_0    pypi
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
django                    5.0.2                    pypi_0    pypi
docutils                  0.20.1          py310hff52083_3    conda-forge
dpath                     2.1.6                    pypi_0    pypi
easel                     0.49                 h031d066_0    bioconda
eggnog-mapper             2.1.12             pyhdfd78af_0    bioconda
entrez-direct             16.2                 he881be0_1    bioconda
ete3                      3.1.3                    pypi_0    pypi
expat                     2.5.0                hcb278e6_1    conda-forge
famsa                     2.2.2                h4ac6f70_2    bioconda
fastani                   1.34                 h4dfc31f_1    bioconda
fastjsonschema            2.19.1                   pypi_0    pypi
fasttree                  2.1.11               h031d066_2    bioconda
fmt                       10.2.1               h00ab1b0_0    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                 h77eed37_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.49.0                   pypi_0    pypi
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gawk                      5.3.0                ha916aea_0    conda-forge
gcc_impl_linux-64         13.2.0               h338b0a0_5    conda-forge
gdk-pixbuf                2.42.10              h6b639ba_2    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    13.2.0               h76e1118_5    conda-forge
ghostscript               10.02.1              h59595ed_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
gitdb                     4.0.11                   pypi_0    pypi
gitpython                 3.1.42                   pypi_0    pypi
gmp                       6.3.0                h59595ed_0    conda-forge
graphite2                 1.3.14               h295c915_1
graphviz                  8.1.0                h28d9a01_0    conda-forge
gsl                       2.7.1                h6e86dc7_1
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h977cf35_4    conda-forge
gxx_impl_linux-64         13.2.0               h338b0a0_5    conda-forge
harfbuzz                  7.3.0                hdb3a94d_0    conda-forge
hmmer                     3.4                  hdbdd923_0    bioconda
htslib                    1.19.1               h81da01d_1    bioconda
humanfriendly             10.0                     pypi_0    pypi
icu                       72.1                 hcb278e6_0    conda-forge
idba                      1.1.3                         1    bioconda
idna                      3.6                pyhd8ed1ab_0    conda-forge
illumina-utils            2.13                     pypi_0    pypi
infernal                  1.1.5           pl5321h031d066_0    bioconda
iqtree                    2.2.6                h21ec9f0_0    bioconda
jinja2                    3.1.3                    pypi_0    pypi
joblib                    1.3.2                    pypi_0    pypi
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
jsonschema                4.21.1                   pypi_0    pypi
jsonschema-specifications 2023.12.1                pypi_0    pypi
jupyter-core              5.7.1                    pypi_0    pypi
kernel-headers_linux-64   3.10.0              h4a8ded7_14    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5                    pypi_0    pypi
kmer-jellyfish            1.1.12               h9f5acd7_2    bioconda
krakenuniq                1.0.4           pl5321h6dccd9a_1    bioconda
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
levenshtein               0.25.0                   pypi_0    pypi
libarchive                3.7.2                h039dbb9_0    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcurl                   8.5.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20230828         h5eee18b_0
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.4                h6a678d5_0
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-devel_linux-64     13.2.0             ha9c7c90_105    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgd                     2.3.3                hfa28ad5_6    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libglib                   2.78.1               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libhwloc                  2.9.3           default_h554bfaf_1009    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libidn2                   2.3.7                hd590300_0    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
liblapacke                3.9.0           21_linux64_openblas    conda-forge
libmamba                  1.5.6                had39da4_0    conda-forge
libmambapy                1.5.6           py310h39ff949_0    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                    1.6.42               h2797004_0    conda-forge
librsvg                   2.56.3               h98fae49_0    conda-forge
libsanitizer              13.2.0               h7e041cc_5    conda-forge
libsolv                   0.7.28               hfc55251_0    conda-forge
libsqlite                 3.45.1               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-devel_linux-64  13.2.0             ha9c7c90_105    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libtiff                   4.5.1                h8b53f26_1    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libunistring              0.9.10               h7f98852_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.44.2               hd590300_1    conda-forge
libwebp                   1.3.1                hbf2b3c1_0    conda-forge
libwebp-base              1.3.1                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.11.5               h0d562d8_0    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvm-openmp               8.0.1                hc9558a2_0    conda-forge
llvmlite                  0.42.0                   pypi_0    pypi
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
make                      4.3                  hd18ef5c_1    conda-forge
mamba                     1.5.6           py310h51d5547_0    conda-forge
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.5                    pypi_0    pypi
matplotlib                3.8.3                    pypi_0    pypi
mcl                       22.282          pl5321h031d066_1    bioconda
mdurl                     0.1.2                    pypi_0    pypi
megahit                   1.2.9                h43eeafb_4    bioconda
meme                      5.5.5           pl5321hda358d9_0    bioconda
menuinst                  2.0.2           py310hff52083_0    conda-forge
metabat2                  2.15                 h986a166_1    bioconda
mistune                   3.0.2                    pypi_0    pypi
mmseqs2                   13.45111        pl5321hf1761c0_2    bioconda
mpfr                      4.2.1                h9458935_0    conda-forge
mpi                       1.0                     openmpi    conda-forge
multiprocess              0.70.16                  pypi_0    pypi
muscle                    3.8.1551             h7d875b9_6    bioconda
nbformat                  5.9.2                    pypi_0    pypi
ncbi-vdb                  3.0.0           pl5321h87f3376_0    bioconda
ncurses                   6.4                  h59595ed_2    conda-forge
networkx                  3.2.1                    pypi_0    pypi
nodejs                    20.5.1               hf52ce11_0    conda-forge
numba                     0.59.0                   pypi_0    pypi
numpy                     1.23.5                   pypi_0    pypi
openmp                    8.0.1                         0    conda-forge
openmpi                   4.1.6              hc5af2df_101    conda-forge
openssl                   3.2.1                hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    1.4.4                    pypi_0    pypi
pandoc                    3.1.12.1             ha770c72_0    conda-forge
pango                     1.50.14              heaa33ce_1    conda-forge
paste                     3.7.1                    pypi_0    pypi
patsy                     0.5.6                    pypi_0    pypi
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
perl-app-cpanminus        1.7047          pl5321hd8ed1ab_0    conda-forge
perl-archive-tar          2.40            pl5321hdfd78af_0    bioconda
perl-base                 2.23            pl5321hd8ed1ab_0    conda-forge
perl-business-isbn        3.007           pl5321hd8ed1ab_0    conda-forge
perl-business-isbn-data   20210112.006    pl5321hd8ed1ab_0    conda-forge
perl-carp                 1.50            pl5321hd8ed1ab_0    conda-forge
perl-cgi                  4.56            pl5321h031d066_1    bioconda
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-constant             1.33            pl5321hd8ed1ab_0    conda-forge
perl-dbi                  1.643           pl5321h166bdaf_0    conda-forge
perl-digest-hmac          1.04            pl5321hdfd78af_0    bioconda
perl-digest-md5           2.58            pl5321h166bdaf_0    conda-forge
perl-encode               3.19            pl5321h166bdaf_0    conda-forge
perl-encode-locale        1.05            pl5321hdfd78af_7    bioconda
perl-exporter             5.74            pl5321hd8ed1ab_0    conda-forge
perl-exporter-tiny        1.002002        pl5321hd8ed1ab_0    conda-forge
perl-extutils-makemaker   7.70            pl5321hd8ed1ab_0    conda-forge
perl-file-listing         6.16            pl5321hdfd78af_0    bioconda
perl-file-path            2.18            pl5321hd8ed1ab_0    conda-forge
perl-file-spec            3.48_01         pl5321hdfd78af_2    bioconda
perl-file-temp            0.2304          pl5321hd8ed1ab_0    conda-forge
perl-file-which           1.24            pl5321hd8ed1ab_0    conda-forge
perl-html-parser          3.81            pl5321h4ac6f70_1    bioconda
perl-html-tagset          3.20            pl5321hdfd78af_4    bioconda
perl-html-template        2.97            pl5321hdfd78af_2    bioconda
perl-html-tree            5.07            pl5321hdfd78af_2    bioconda
perl-http-cookies         6.10            pl5321hdfd78af_0    bioconda
perl-http-daemon          6.16            pl5321hdfd78af_0    bioconda
perl-http-date            6.06            pl5321hdfd78af_0    bioconda
perl-http-message         6.36            pl5321hdfd78af_0    bioconda
perl-http-negotiate       6.01            pl5321hdfd78af_4    bioconda
perl-inc-latest           0.500           pl5321ha770c72_0    conda-forge
perl-io-compress          2.201           pl5321hdbdd923_2    bioconda
perl-io-html              1.004           pl5321hdfd78af_0    bioconda
perl-io-socket-ssl        2.075           pl5321hd8ed1ab_0    conda-forge
perl-io-zlib              1.14            pl5321hdfd78af_0    bioconda
perl-json                 4.10            pl5321hdfd78af_0    bioconda
perl-json-xs              2.34            pl5321h4ac6f70_6    bioconda
perl-libwww-perl          6.67            pl5321hdfd78af_0    bioconda
perl-list-moreutils       0.430           pl5321hdfd78af_0    bioconda
perl-list-moreutils-xs    0.430           pl5321h031d066_2    bioconda
perl-log-log4perl         1.56            pl5321hd8ed1ab_0    conda-forge
perl-lwp-mediatypes       6.04            pl5321hdfd78af_1    bioconda
perl-lwp-protocol-https   6.10            pl5321hdfd78af_0    bioconda
perl-math-cdf             0.1             pl5321h031d066_9    bioconda
perl-mime-base64          3.16            pl5321h166bdaf_0    conda-forge
perl-module-build         0.4234          pl5321ha770c72_0    conda-forge
perl-mozilla-ca           20211001        pl5321hdfd78af_0    bioconda
perl-net-http             6.22            pl5321hdfd78af_0    bioconda
perl-net-ssleay           1.92            pl5321hf14f497_1    conda-forge
perl-ntlm                 1.09            pl5321hdfd78af_5    bioconda
perl-parent               0.241           pl5321hd8ed1ab_0    conda-forge
perl-pathtools            3.75            pl5321h166bdaf_0    conda-forge
perl-scalar-list-utils    1.63            pl5321h166bdaf_0    conda-forge
perl-socket               2.027           pl5321h031d066_4    bioconda
perl-storable             3.15            pl5321h166bdaf_0    conda-forge
perl-sys-info             0.7811          pl5321hdfd78af_1    bioconda
perl-sys-info-base        0.7807          pl5321hdfd78af_1    bioconda
perl-sys-info-driver-linux 0.7905          pl5321hdfd78af_1    bioconda
perl-test-fatal           0.016           pl5321ha770c72_0    conda-forge
perl-test-nowarnings      1.06            pl5321ha770c72_0    conda-forge
perl-test-requiresinternet 0.05            pl5321hdfd78af_1    bioconda
perl-test-warnings        0.031           pl5321ha770c72_0    conda-forge
perl-text-template-simple 0.91            pl5321hdfd78af_1    bioconda
perl-time-local           1.35            pl5321hdfd78af_0    bioconda
perl-timedate             2.33            pl5321hdfd78af_2    bioconda
perl-try-tiny             0.31            pl5321ha770c72_0    conda-forge
perl-types-serialiser     1.01            pl5321hdfd78af_0    bioconda
perl-unix-processors      2.046           pl5321h7f98852_1001    conda-forge
perl-uri                  5.17            pl5321ha770c72_0    conda-forge
perl-url-encode           0.03            pl5321h9ee0642_0    bioconda
perl-www-robotrules       6.02            pl5321hdfd78af_4    bioconda
perl-xml-namespacesupport 1.12            pl5321hd8ed1ab_0    conda-forge
perl-xml-parser           2.44_01         pl5321hc3e0081_1003    conda-forge
perl-xml-sax              1.02            pl5321hd8ed1ab_0    conda-forge
perl-xml-sax-base         1.09            pl5321hd8ed1ab_0    conda-forge
perl-xml-sax-expat        0.51            pl5321hd8ed1ab_0    conda-forge
perl-xml-simple           2.25            pl5321hdfd78af_2    bioconda
perl-yaml                 1.30            pl5321hdfd78af_0    bioconda
pillow                    10.2.0                   pypi_0    pypi
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
plac                      1.4.2                    pypi_0    pypi
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
plotext                   5.2.8                    pypi_0    pypi
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
popt                      1.16                          1    bioconda
prodigal                  2.6.3                h031d066_7    bioconda
psutil                    5.9.8           py310h2372a71_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pulp                      2.8.0                    pypi_0    pypi
pyani                     0.2.12                   pypi_0    pypi
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.17.2                   pypi_0    pypi
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysam                     0.22.0                   pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.13         hd12c33a_1_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python-levenshtein        0.25.0                   pypi_0    pypi
python_abi                3.10                    4_cp310    conda-forge
pytz                      2024.1                   pypi_0    pypi
pyyaml                    6.0.1                    pypi_0    pypi
r-askpass                 1.2.0             r43h57805ef_0    conda-forge
r-assertthat              0.2.1             r43hc72bb7e_4    conda-forge
r-backports               1.4.1             r43h57805ef_2    conda-forge
r-base                    4.3.1                h29c4799_3    conda-forge
r-base64enc               0.1_3           r43h57805ef_1006    conda-forge
r-bit                     4.0.5             r43h57805ef_1    conda-forge
r-bit64                   4.0.5             r43h57805ef_2    conda-forge
r-blob                    1.2.4             r43hc72bb7e_1    conda-forge
r-broom                   1.0.5             r43hc72bb7e_1    conda-forge
r-bslib                   0.6.1             r43hc72bb7e_0    conda-forge
r-cachem                  1.0.8             r43h57805ef_1    conda-forge
r-callr                   3.7.5             r43hc72bb7e_0    conda-forge
r-cellranger              1.1.0           r43hc72bb7e_1006    conda-forge
r-cli                     3.6.2             r43ha503ecb_0    conda-forge
r-clipr                   0.8.0             r43hc72bb7e_2    conda-forge
r-colorspace              2.1_0             r43h57805ef_1    conda-forge
r-conflicted              1.2.0             r43h785f33e_1    conda-forge
r-cpp11                   0.4.7             r43hc72bb7e_0    conda-forge
r-crayon                  1.5.2             r43hc72bb7e_2    conda-forge
r-curl                    5.1.0             r43hf9611b0_0    conda-forge
r-data.table              1.14.10           r43h029312a_1    conda-forge
r-dbi                     1.2.2             r43hc72bb7e_0    conda-forge
r-dbplyr                  2.4.0             r43hc72bb7e_0    conda-forge
r-digest                  0.6.34            r43ha503ecb_0    conda-forge
r-dplyr                   1.1.4             r43ha503ecb_0    conda-forge
r-dtplyr                  1.3.1             r43hc72bb7e_1    conda-forge
r-ellipsis                0.3.2             r43h57805ef_2    conda-forge
r-evaluate                0.23              r43hc72bb7e_0    conda-forge
r-fansi                   1.0.6             r43h57805ef_0    conda-forge
r-farver                  2.1.1             r43ha503ecb_2    conda-forge
r-fastmap                 1.1.1             r43ha503ecb_1    conda-forge
r-fontawesome             0.5.2             r43hc72bb7e_0    conda-forge
r-forcats                 1.0.0             r43hc72bb7e_1    conda-forge
r-fs                      1.6.3             r43ha503ecb_0    conda-forge
r-gargle                  1.5.2             r43h785f33e_0    conda-forge
r-generics                0.1.3             r43hc72bb7e_2    conda-forge
r-getopt                  1.20.4            r43ha770c72_0    conda-forge
r-ggplot2                 3.4.4             r43hc72bb7e_0    conda-forge
r-glue                    1.7.0             r43h57805ef_0    conda-forge
r-googledrive             2.1.1             r43hc72bb7e_1    conda-forge
r-googlesheets4           1.1.1             r43h785f33e_1    conda-forge
r-gtable                  0.3.4             r43hc72bb7e_0    conda-forge
r-haven                   2.5.4             r43ha503ecb_0    conda-forge
r-highr                   0.10              r43hc72bb7e_1    conda-forge
r-hms                     1.1.3             r43hc72bb7e_1    conda-forge
r-htmltools               0.5.7             r43ha503ecb_0    conda-forge
r-httr                    1.4.7             r43hc72bb7e_0    conda-forge
r-ids                     1.0.1             r43hc72bb7e_3    conda-forge
r-isoband                 0.2.7             r43ha503ecb_2    conda-forge
r-jquerylib               0.1.4             r43hc72bb7e_2    conda-forge
r-jsonlite                1.8.8             r43h57805ef_0    conda-forge
r-knitr                   1.45              r43hc72bb7e_0    conda-forge
r-labeling                0.4.3             r43hc72bb7e_0    conda-forge
r-lattice                 0.22_5            r43h57805ef_0    conda-forge
r-lifecycle               1.0.4             r43hc72bb7e_0    conda-forge
r-lubridate               1.9.3             r43h57805ef_0    conda-forge
r-magrittr                2.0.3             r43h57805ef_2    conda-forge
r-mass                    7.3_60            r43h57805ef_1    conda-forge
r-matrix                  1.6_5             r43h316c678_0    conda-forge
r-memoise                 2.0.1             r43hc72bb7e_2    conda-forge
r-mgcv                    1.9_1             r43h316c678_0    conda-forge
r-mime                    0.12              r43h57805ef_2    conda-forge
r-modelr                  0.1.11            r43hc72bb7e_1    conda-forge
r-munsell                 0.5.0           r43hc72bb7e_1006    conda-forge
r-nlme                    3.1_164           r43h61816a4_0    conda-forge
r-openssl                 2.1.1             r43hb353fa6_0    conda-forge
r-optparse                1.7.4             r43hc72bb7e_0    conda-forge
r-pillar                  1.9.0             r43hc72bb7e_1    conda-forge
r-pkgconfig               2.0.3             r43hc72bb7e_3    conda-forge
r-plyr                    1.8.9             r43ha503ecb_0    conda-forge
r-prettyunits             1.2.0             r43hc72bb7e_0    conda-forge
r-processx                3.8.3             r43h57805ef_0    conda-forge
r-progress                1.2.3             r43hc72bb7e_0    conda-forge
r-ps                      1.7.6             r43h57805ef_0    conda-forge
r-purrr                   1.0.2             r43h57805ef_0    conda-forge
r-r6                      2.5.1             r43hc72bb7e_2    conda-forge
r-ragg                    1.2.6             r43h884c59f_0
r-rappdirs                0.3.3             r43h57805ef_2    conda-forge
r-rcolorbrewer            1.1_3             r43h785f33e_2    conda-forge
r-rcpp                    1.0.12            r43h7df8631_0    conda-forge
r-readr                   2.1.5             r43ha503ecb_0    conda-forge
r-readxl                  1.4.3             r43ha5c9fba_0    conda-forge
r-rematch                 2.0.0             r43hc72bb7e_0    conda-forge
r-rematch2                2.1.2             r43hc72bb7e_3    conda-forge
r-reprex                  2.1.0             r43hc72bb7e_0    conda-forge
r-reshape2                1.4.4             r43ha503ecb_3    conda-forge
r-rlang                   1.1.3             r43ha503ecb_0    conda-forge
r-rmarkdown               2.25              r43hc72bb7e_0    conda-forge
r-rstudioapi              0.15.0            r43hc72bb7e_0    conda-forge
r-rvest                   1.0.4             r43hc72bb7e_0    conda-forge
r-sass                    0.4.8             r43ha503ecb_0    conda-forge
r-scales                  1.3.0             r43hc72bb7e_0    conda-forge
r-selectr                 0.4_2             r43hc72bb7e_3    conda-forge
r-stringi                 1.7.12            r43hc0c3e09_2    conda-forge
r-stringr                 1.5.1             r43h785f33e_0    conda-forge
r-sys                     3.4.2             r43h57805ef_1    conda-forge
r-systemfonts             1.0.5             r43haf97adc_0    conda-forge
r-textshaping             0.3.7             r43h884c59f_0
r-tibble                  3.2.1             r43h57805ef_2    conda-forge
r-tidyr                   1.3.1             r43ha503ecb_0    conda-forge
r-tidyselect              1.2.0             r43hc72bb7e_1    conda-forge
r-tidyverse               2.0.0             r43h785f33e_1    conda-forge
r-timechange              0.3.0             r43ha503ecb_0    conda-forge
r-tinytex                 0.49              r43hc72bb7e_1    conda-forge
r-tzdb                    0.4.0             r43ha503ecb_1    conda-forge
r-utf8                    1.2.4             r43h57805ef_0    conda-forge
r-uuid                    1.2_0             r43h57805ef_0    conda-forge
r-vctrs                   0.6.5             r43ha503ecb_0    conda-forge
r-viridislite             0.4.2             r43hc72bb7e_1    conda-forge
r-vroom                   1.6.5             r43ha503ecb_0    conda-forge
r-withr                   3.0.0             r43hc72bb7e_0    conda-forge
r-xfun                    0.42              r43ha503ecb_0    conda-forge
r-xml2                    1.3.5             r43h1ad5fc0_0    conda-forge
r-yaml                    2.3.8             r43h57805ef_0    conda-forge
rapidfuzz                 3.6.1                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.33.0                   pypi_0    pypi
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
reretry                   0.11.8                   pypi_0    pypi
rich                      13.7.0                   pypi_0    pypi
rich-argparse             1.4.0                    pypi_0    pypi
rpds-py                   0.18.0                   pypi_0    pypi
rsync                     3.2.7                h70740c4_0    conda-forge
ruamel.yaml               0.18.6          py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.8           py310h2372a71_0    conda-forge
samtools                  1.19.2               h50ea8bc_0    bioconda
scikit-learn              1.2.2                    pypi_0    pypi
scipy                     1.12.0                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
sed                       4.8                  he412f7d_0    conda-forge
setuptools                69.1.0             pyhd8ed1ab_1    conda-forge
six                       1.16.0                   pypi_0    pypi
smart-open                6.4.0                    pypi_0    pypi
smmap                     5.0.1                    pypi_0    pypi
snakemake                 7.32.4                   pypi_0    pypi
spades                    3.15.5               h95f258a_1    bioconda
sqlite                    3.45.1               h2c6b66d_0    conda-forge
sqlparse                  0.4.4                    pypi_0    pypi
statsmodels               0.14.1                   pypi_0    pypi
stopit                    1.1.2                    pypi_0    pypi
sysroot_linux-64          2.17                h4a8ded7_14    conda-forge
tabulate                  0.9.0                    pypi_0    pypi
tar                       1.34                 hb2e2bae_1    conda-forge
tbb                       2021.11.0            h00ab1b0_1    conda-forge
threadpoolctl             3.3.0                    pypi_0    pypi
throttler                 1.2.2                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tktable                   2.10                 h0c5db8f_5    conda-forge
toposort                  1.10                     pypi_0    pypi
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.1                   pypi_0    pypi
trimal                    1.4.1                h4ac6f70_8    bioconda
trnascan-se               2.0.12          pl5321h031d066_0    bioconda
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
typing-extensions         4.9.0                    pypi_0    pypi
tzdata                    2024a                h0c530f3_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
vmatch                    2.3.0                hec16e2b_5    bioconda
wget                      1.21.4               h251f7ec_1
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0                   pypi_0    pypi
xlsxwriter                3.1.9              pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.7                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxt                1.3.0                hd590300_1    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xxhash                    0.8.0                h7f98852_3    conda-forge
xz                        5.4.5                h5eee18b_0
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
yte                       1.5.4                    pypi_0    pypi
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.22.0          py310h1275a96_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Detailed description of the issue

I included the following section in the workflow. I may be wrong on the entries I made in the anv_script part, but it bugs out running emapper.py. Perhaps it's relevant so I include it.

    "emapper": {
        "--database": [ "bact", "arch", "euk" ],
        "--usemem": true,
        "--override": true,
        "path_to_emapper_dir": "",
        "threads": 30
    },
    "anvi_script_run_eggnog_mapper": {
        "--use-version": "1.0.3",
        "run": true,
        "--cog-data-dir": "/Taxonomy/802/anvio-8-eggnogmapper",
        "--drop-previous-annotations": "",
        "threads": 30
    },

Note: I have tried multiple variations of the database & emapper_dir options, none seemed to advance the script.

Structure in /Taxonomy/802/anvio-8-eggnogmapper

/Taxonomy/802/anvio-8-eggnogmapper$ ls
eggnog.db  eggnog_proteins.dmnd  eggnog.taxa.db  eggnog.taxa.db.traverse.pkl

When running the workflow:

python2.7 /usr/local/bin/miniconda3/envs/anvio-8/bin/emapper.py -i 03_CONTIGS/G01-contigs-aa-sequences.fa --output 03_CONTIGS/G01-contigs --cpu 30 --database ['bact', 'arch', 'euk'] --usemem --override >> 00_LOGS/G01-emapper.log 2>&1
[Thu Feb 29 14:20:35 2024]
Error in rule emapper:
    jobid: 0
    input: 03_CONTIGS/G01-contigs-aa-sequences.fa
    output: 03_CONTIGS/G01-contigs.emapper.annotations
    log: 00_LOGS/G01-emapper.log (check log file(s) for error details)

RuleException:
CalledProcessError in file /usr/local/bin/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/contigs/Snakefile, line 449:
Command 'set -euo pipefail;  python2.7 /usr/local/bin/miniconda3/envs/anvio-8/bin/emapper.py -i 03_CONTIGS/G01-contigs-aa-sequences.fa --output 03_CONTIGS/G01-contigs --cpu 30 --database ['bact', 'arch', 'euk'] --usemem --override >> 00_LOGS/G01-emapper.log 2>&1' returned non-zero exit status 1.
  File "/usr/local/bin/miniconda3/envs/anvio-8/lib/python3.10/site-packages/anvio/workflows/contigs/Snakefile", line 449, in __rule_emapper
  File "/usr/local/bin/miniconda3/envs/anvio-8/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-02-29T114100.256539.snakemake.log

There's nothing descriptive in the log. I think the biggest pointer here is python2.7 being called while eggnog mapper requires python 3 (which runs on the system and is included in the installation). No clue why python 2 is being called.

I can run the following manually, which works from within the anvio environment:

(anvio-8) emapper.py  -i 03_CONTIGS/G01-contigs-aa-sequences.fa --output 03_CONTIGS/G01-contigs --cpu 30 --data_dir /Taxonomy/802/anvio-8-eggnogmapper
  /usr/local/bin/miniconda3/envs/anvio-8/bin/diamond blastp -d '/Taxonomy/802/anvio-8-eggnogmapper/eggnog_proteins.dmnd' -q '/Projects/G01-contigs-aa-sequences.fa' --threads 30 -o '/Projects/03_CONTIGS/G01-contigs.emapper.hits' --tmpdir '/Projects/emappertmp_dmdn_1g_5bp8h' --sensitive --iterate -e 0.001 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp

Another pointer here is the --data_dir, a flag which is absent in the default workflow.

Perhaps I'm missing something obvious here, if anyone could share the eggnog part of their workflow, preferably with a custom database location and with a bac/arch installation, that could already help.

Thanks a lot!

[meren]

Hi @timternetnet, I'm sorry you run into this issue. The fact that the emapper rule in our snakemake workflows was still calling python 2.7 was certainly a bug, which I just fixed, and if you were to track the anvi'o development branch (installation instructions here), you can see if it changes anything for you.

But there is a bigger problem with the emapper rule. Emapper used to call sys.exit() at the end of its run to shutdown all lingering threads quickly, which made it impossible to use from within other workflows. I had raised this with its developers a few years ago but at that time they had offered no other solution, so we left the hook in our Snakemake rules, but we stopped using it.

As a workaround we resorted to running it manually by first getting all the gene amino acid sequences from a given contigs-db like this:

anvi-get-sequences-for-gene-calls -c CONTIGS.db \
                                    --get-aa-sequences \
                                    -o amino-acid-sequences.fa

Then running emapper manually as instructed in its tutorial, and then importing the results back into the contigs-db:

anvi-script-run-eggnog-mapper -c CONTIGS.db \
                              --annotation amino-acid-sequences.fa.emapper.annotations \
                              --use-version VERSION

Where VERSION can be any of the versions listed in the help menu, which currently includes 2.0.0, 2.0.1, 2.0.5, 2.1.4, 2.1.6, 2.1.8, and 2.1.9, and can easily be extended to newer versions.

I am not sure if the sys.exit() problem was resolved in newer versions. If it is resolved, the anvi'o program to run emapper and import its results should work without any issue. If it is not resolved, then it is normal that it shuts down the entire snakemake workflow :/

Please let us know if you discover something and whether there is anything we can do to make your life easier. But in the meantime I'm going to close the issue pending input from you.

Best wishes,