[BUG] Eggnog mapper not running in workflow, works fine manually in same conda env
timternetnet opened this issue · comments
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
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rapidfuzz 3.6.1 pypi_0 pypi
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reproc 14.2.4.post0 hd590300_1 conda-forge
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requests 2.31.0 pyhd8ed1ab_0 conda-forge
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rich 13.7.0 pypi_0 pypi
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samtools 1.19.2 h50ea8bc_0 bioconda
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sqlite 3.45.1 h2c6b66d_0 conda-forge
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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!
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,