Closed Laura-Alex closed 2 years ago
meren
commented
2 years ago Hi @Laura-Alex, anvi'o v7.1 is out, your bug is in v6.1. We don't have the people numbers to be able to support earlier versions of anvi'o. But there is no reason to not update to the latest version since we have database migration tools that help you seamlessly continue your research even if you had been using an earlier version of anvi'o on a project.
So my solution is: "please install v7.1" :)
Laura-Alex
commented
2 years ago Hello, and thank you!
I have ran 'conda update anvio' to get version 7 (I'm not sure if it is 7.1, or if 7.1 is not available via conda)
Unfortunately I have the same issue, except now the anvio self-test crashes immediately with a very similar error message as before (instead of running for a while and then crashing).
The error message:
Traceback (most recent call last):
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/utils/timezone.py", line 10, in <module>
import zoneinfo
ModuleNotFoundError: No module named 'zoneinfo'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/anvio/summaryhtml.py", line 46, in <module>
from django.template.loader import render_to_string
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/template/__init__.py", line 44, in <module>
from .engine import Engine
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/template/engine.py", line 7, in <module>
from .base import Template
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/template/base.py", line 59, in <module>
from django.utils.formats import localize
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/utils/formats.py", line 9, in <module>
from django.utils import dateformat, numberformat
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/utils/dateformat.py", line 21, in <module>
from django.utils.timezone import (
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/django/utils/timezone.py", line 12, in <module>
from backports import zoneinfo
ModuleNotFoundError: No module named 'backports'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/[username]/.conda/envs/anvio/bin/anvi-self-test", line 91, in <module>
from anvio.argparse import ArgumentParser
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/anvio/argparse.py", line 15, in <module>
from anvio.programs import Program
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/anvio/programs.py", line 21, in <module>
from anvio.summaryhtml import SummaryHTMLOutput
File "/home/[username]/.conda/envs/anvio/lib/python3.6/site-packages/anvio/summaryhtml.py", line 49, in <module>
raise ConfigError('You need to have Django module (http://djangoproject.com) installed on your system to generate HTML output.')
anvio.errors.ConfigError:
Config Error: You need to have Django module (http://djangoproject.com) installed on your
system to generate HTML output.The output of conda list:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
anvio 7 hdfd78af_1 bioconda
anvio-minimal 7 py_0 bioconda
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
asgiref 3.4.1 pyhd8ed1ab_0 conda-forge
attrs 21.2.0 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_2 conda-forge
bioconductor-qvalue 2.22.0 r40hdfd78af_1 bioconda
biopython 1.79 py36h8f6f2f9_0 conda-forge
blas 1.1 openblas conda-forge
blast 2.11.0 pl526he19e7b1_0 bioconda
blast-legacy 2.2.26 h9ee0642_3 bioconda
boost 1.70.0 py36h9de70de_1 conda-forge
boost-cpp 1.70.0 h7b93d67_3 conda-forge
bottle 0.12.18 py_0 conda-forge
bowtie2 2.4.4 py36hd4290be_0 bioconda
brotlipy 0.7.0 py36h8f6f2f9_1001 conda-forge
bwa 0.7.17 h5bf99c6_8 bioconda
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
centrifuge 1.0.4_beta py36pl526he941832_2 bioconda
certifi 2021.5.30 py36h5fab9bb_0 conda-forge
cffi 1.14.6 py36hd8eec40_1 conda-forge
charset-normalizer 2.0.9 pyhd8ed1ab_0 conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
colored 1.4.2 py_0 conda-forge
conda 4.10.3 py36h5fab9bb_2 conda-forge
conda-package-handling 1.7.3 py36h8f6f2f9_0 conda-forge
configargparse 1.5.3 pyhd8ed1ab_0 conda-forge
cryptography 35.0.0 py36hb60f036_0 conda-forge
curl 7.76.1 h979ede3_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
datrie 0.8.2 py36h8f6f2f9_2 conda-forge
dbus 1.13.6 h48d8840_2 conda-forge
decorator 5.1.0 pyhd8ed1ab_0 conda-forge
diamond 0.9.14 h2e03b76_4 bioconda
django 4.0 pyhd8ed1ab_0 conda-forge
docutils 0.17.1 py36h5fab9bb_0 conda-forge
entrez-direct 16.2 he881be0_0 bioconda
ete3 3.1.2 pyh9f0ad1d_0 conda-forge
expat 2.4.1 h9c3ff4c_0 conda-forge
fastani 1.32 he1c1bb9_0 bioconda
fasttree 2.1.10 h779adbc_5 bioconda
fontconfig 2.13.1 hba837de_1005 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gcc_linux-64 9.4.0 h391b98a_2 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
gfortran_impl_linux-64 9.4.0 h0003116_11 conda-forge
gfortran_linux-64 9.4.0 hf0ab688_2 conda-forge
gitdb 4.0.9 pyhd8ed1ab_0 conda-forge
gitpython 3.1.18 pyhd8ed1ab_0 conda-forge
glib 2.70.2 h780b84a_0 conda-forge
glib-tools 2.70.2 h780b84a_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gsl 2.6 he838d99_2 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.18.5 h9f60fe5_2 conda-forge
gxx_impl_linux-64 9.4.0 h03d3576_11 conda-forge
gxx_linux-64 9.4.0 h0316aca_2 conda-forge
harfbuzz 2.7.2 ha5b49bf_1 conda-forge
hmmer 3.3.2 h1b792b2_1 bioconda
htslib 1.12 h9093b5e_1 bioconda
icu 67.1 he1b5a44_0 conda-forge
idna 3.1 pyhd3deb0d_0 conda-forge
illumina-utils 2.12 pyhdfd78af_0 bioconda
importlib-metadata 4.8.1 py36h5fab9bb_0 conda-forge
infernal 1.1.4 h779adbc_0 bioconda
ipython_genutils 0.2.0 py_1 conda-forge
iqtree 2.1.4_beta hdcc8f71_0 bioconda
jpeg 9d h36c2ea0_0 conda-forge
jsonschema 4.1.2 pyhd8ed1ab_0 conda-forge
jupyter_core 4.8.1 py36h5fab9bb_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
kiwisolver 1.3.1 py36h605e78d_1 conda-forge
krb5 1.17.2 h926e7f8_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libarchive 3.5.1 h3f442fb_1 conda-forge
libblas 3.9.0 1_h86c2bf4_netlib conda-forge
libcblas 3.9.0 5_h92ddd45_netlib conda-forge
libclang 11.1.0 default_ha53f305_1 conda-forge
libcurl 7.76.1 hc4aaa36_1 conda-forge
libdeflate 1.7 h7f98852_5 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libgcc-ng 11.2.0 h1d223b6_11 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 11.2.0 h69a702a_11 conda-forge
libgfortran5 11.2.0 h5c6108e_11 conda-forge
libglib 2.70.2 h174f98d_0 conda-forge
libgomp 11.2.0 h1d223b6_11 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 5_h92ddd45_netlib conda-forge
libllvm10 10.0.1 he513fc3_3 conda-forge
libllvm11 11.1.0 hf817b99_2 conda-forge
libnghttp2 1.43.0 h812cca2_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 12.3 h255efa7_3 conda-forge
libsanitizer 9.4.0 h79bfe98_11 conda-forge
libsolv 0.7.19 h780b84a_5 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.4.0 hd854feb_11 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_11 conda-forge
libtiff 4.2.0 hbd63e13_2 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.1 h7f98852_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
libxslt 1.1.33 hf705e74_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
llvmlite 0.36.0 py36h05121d2_0 conda-forge
lxml 4.6.3 py36h04a5ba7_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mamba 0.13.0 py36h05d92e0_0 conda-forge
matplotlib-base 3.3.4 py36hd391965_0 conda-forge
mcl 14.137 pl5262h779adbc_6 bioconda
megahit 1.2.9 h2e03b76_1 bioconda
mistune 2.0.0 pyhd8ed1ab_1 conda-forge
mummer 3.23 pl5262h1b792b2_12 bioconda
muscle 3.8.1551 h7d875b9_6 bioconda
mysql-common 8.0.25 ha770c72_0 conda-forge
mysql-libs 8.0.25 h935591d_0 conda-forge
nbformat 5.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
nspr 4.32 h9c3ff4c_1 conda-forge
nss 3.73 hb5efdd6_0 conda-forge
numba 0.53.1 py36h1328434_1 conda-forge
numpy 1.19.5 py36hfc0c790_2 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openblas 0.2.20 8 conda-forge
openssl 1.1.1l h7f98852_0 conda-forge
pandas 0.25.1 py36hb3f55d8_0 conda-forge
pandoc 2.16.2 h7f98852_0 conda-forge
pango 1.42.4 h69149e4_5 conda-forge
paste 3.5.0 pyh9f0ad1d_0 conda-forge
patsy 0.5.2 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.36 h032f7d1_1 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
perl-archive-tar 2.32 pl526_0 bioconda
perl-carp 1.38 pl526_3 bioconda
perl-common-sense 3.74 pl526_2 bioconda
perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda
perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda
perl-exporter 5.72 pl526_1 bioconda
perl-exporter-tiny 1.002001 pl526_0 bioconda
perl-extutils-makemaker 7.36 pl526_1 bioconda
perl-io-compress 2.087 pl526he1b5a44_0 bioconda
perl-io-zlib 1.10 pl526_2 bioconda
perl-json 4.02 pl526_0 bioconda
perl-json-xs 2.34 pl526h6bb024c_3 bioconda
perl-list-moreutils 0.428 pl526_1 bioconda
perl-list-moreutils-xs 0.428 pl526_0 bioconda
perl-pathtools 3.75 pl526h14c3975_1 bioconda
perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda
perl-types-serialiser 1.0 pl526_2 bioconda
perl-xsloader 0.24 pl526_0 bioconda
pillow 7.2.0 py36h8328e55_2 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
prodigal 2.6.3 h779adbc_3 bioconda
psutil 5.4.3 py36_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyani 0.2.10 py_0 bioconda
pycosat 0.6.3 py36h8f6f2f9_1006 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.6 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py36h5fab9bb_7 conda-forge
pyqt-impl 5.12.3 py36h7ec31b9_7 conda-forge
pyqt5-sip 4.19.18 py36hc4f0c31_7 conda-forge
pyqtchart 5.12 py36h7ec31b9_7 conda-forge
pyqtwebengine 5.12.1 py36h7ec31b9_7 conda-forge
pyrsistent 0.17.3 py36h8f6f2f9_2 conda-forge
pysam 0.16.0.1 py36h61e5637_3 bioconda
pysocks 1.7.1 py36h5fab9bb_3 conda-forge
python 3.6.15 hb7a2778_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-levenshtein 0.12.2 py36h8f6f2f9_0 conda-forge
python_abi 3.6 2_cp36m conda-forge
pytz 2021.3 pyhd8ed1ab_0 conda-forge
pyyaml 5.4.1 py36h8f6f2f9_1 conda-forge
qt 5.12.9 h763d07f_1 conda-forge
r-askpass 1.1 r40hcfec24a_2 conda-forge
r-assertthat 0.2.1 r40hc72bb7e_2 conda-forge
r-backports 1.4.0 r40hcfec24a_0 conda-forge
r-base 4.0.3 ha43b4e8_3 conda-forge
r-base64enc 0.1_3 r40hcfec24a_1004 conda-forge
r-bit 4.0.4 r40hcfec24a_0 conda-forge
r-bit64 4.0.5 r40hcfec24a_0 conda-forge
r-blob 1.2.2 r40hc72bb7e_0 conda-forge
r-brio 1.1.3 r40hcfec24a_0 conda-forge
r-broom 0.7.10 r40hc72bb7e_0 conda-forge
r-callr 3.7.0 r40hc72bb7e_0 conda-forge
r-cellranger 1.1.0 r40hc72bb7e_1003 conda-forge
r-cli 3.1.0 r40h03ef668_0 conda-forge
r-clipr 0.7.1 r40hc72bb7e_0 conda-forge
r-colorspace 2.0_2 r40hcfec24a_0 conda-forge
r-cpp11 0.4.2 r40hc72bb7e_0 conda-forge
r-crayon 1.4.2 r40hc72bb7e_0 conda-forge
r-curl 4.3.2 r40hcfec24a_0 conda-forge
r-data.table 1.14.2 r40hcfec24a_0 conda-forge
r-dbi 1.1.1 r40hc72bb7e_0 conda-forge
r-dbplyr 2.1.1 r40hc72bb7e_0 conda-forge
r-desc 1.4.0 r40hc72bb7e_0 conda-forge
r-diffobj 0.3.5 r40hcfec24a_0 conda-forge
r-digest 0.6.29 r40h03ef668_0 conda-forge
r-dplyr 1.0.7 r40h03ef668_0 conda-forge
r-dtplyr 1.2.0 r40hc72bb7e_0 conda-forge
r-ellipsis 0.3.2 r40hcfec24a_0 conda-forge
r-evaluate 0.14 r40hc72bb7e_2 conda-forge
r-fansi 0.5.0 r40hcfec24a_0 conda-forge
r-farver 2.1.0 r40h03ef668_0 conda-forge
r-fastmap 1.1.0 r40h03ef668_0 conda-forge
r-forcats 0.5.1 r40hc72bb7e_0 conda-forge
r-fs 1.5.2 r40h03ef668_0 conda-forge
r-gargle 1.2.0 r40hc72bb7e_0 conda-forge
r-generics 0.1.1 r40hc72bb7e_0 conda-forge
r-getopt 1.20.3 r40ha770c72_2 conda-forge
r-ggplot2 3.3.5 r40hc72bb7e_0 conda-forge
r-glue 1.5.1 r40hcfec24a_0 conda-forge
r-googledrive 2.0.0 r40hc72bb7e_0 conda-forge
r-googlesheets4 1.0.0 r40h785f33e_0 conda-forge
r-gtable 0.3.0 r40hc72bb7e_3 conda-forge
r-haven 2.4.3 r40h2713e49_0 conda-forge
r-highr 0.9 r40hc72bb7e_0 conda-forge
r-hms 1.1.1 r40hc72bb7e_0 conda-forge
r-htmltools 0.5.2 r40h03ef668_0 conda-forge
r-httr 1.4.2 r40hc72bb7e_0 conda-forge
r-ids 1.0.1 r40hc72bb7e_1 conda-forge
r-isoband 0.2.5 r40h03ef668_0 conda-forge
r-jquerylib 0.1.4 r40hc72bb7e_0 conda-forge
r-jsonlite 1.7.2 r40hcfec24a_0 conda-forge
r-knitr 1.36 r40hc72bb7e_0 conda-forge
r-labeling 0.4.2 r40hc72bb7e_0 conda-forge
r-lattice 0.20_45 r40hcfec24a_0 conda-forge
r-lifecycle 1.0.1 r40hc72bb7e_0 conda-forge
r-lubridate 1.8.0 r40h03ef668_0 conda-forge
r-magrittr 2.0.1 r40hcfec24a_1 conda-forge
r-markdown 1.1 r40hcfec24a_1 conda-forge
r-mass 7.3_54 r40hcfec24a_0 conda-forge
r-matrix 1.4_0 r40he454529_0 conda-forge
r-mgcv 1.8_38 r40he454529_0 conda-forge
r-mime 0.12 r40hcfec24a_0 conda-forge
r-modelr 0.1.8 r40hc72bb7e_0 conda-forge
r-munsell 0.5.0 r40hc72bb7e_1003 conda-forge
r-nlme 3.1_153 r40h859d828_0 conda-forge
r-openssl 1.4.5 r40he36bf35_1 conda-forge
r-optparse 1.7.1 r40hc72bb7e_0 conda-forge
r-pillar 1.6.4 r40hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r40hc72bb7e_1 conda-forge
r-pkgload 1.2.4 r40h03ef668_0 conda-forge
r-plyr 1.8.6 r40h03ef668_1 conda-forge
r-praise 1.0.0 r40hc72bb7e_1004 conda-forge
r-prettyunits 1.1.1 r40hc72bb7e_1 conda-forge
r-processx 3.5.2 r40hcfec24a_0 conda-forge
r-progress 1.2.2 r40hc72bb7e_2 conda-forge
r-ps 1.6.0 r40hcfec24a_0 conda-forge
r-purrr 0.3.4 r40hcfec24a_1 conda-forge
r-r6 2.5.1 r40hc72bb7e_0 conda-forge
r-rappdirs 0.3.3 r40hcfec24a_0 conda-forge
r-rcolorbrewer 1.1_2 r40h785f33e_1003 conda-forge
r-rcpp 1.0.7 r40h03ef668_0 conda-forge
r-readr 2.1.1 r40h03ef668_0 conda-forge
r-readxl 1.3.1 r40h2713e49_4 conda-forge
r-rematch 1.0.1 r40hc72bb7e_1003 conda-forge
r-rematch2 2.1.2 r40hc72bb7e_1 conda-forge
r-reprex 2.0.1 r40hc72bb7e_0 conda-forge
r-reshape2 1.4.4 r40h03ef668_1 conda-forge
r-rlang 0.4.12 r40hcfec24a_0 conda-forge
r-rmarkdown 2.11 r40hc72bb7e_0 conda-forge
r-rprojroot 2.0.2 r40hc72bb7e_0 conda-forge
r-rstudioapi 0.13 r40hc72bb7e_0 conda-forge
r-rvest 1.0.2 r40hc72bb7e_0 conda-forge
r-scales 1.1.1 r40hc72bb7e_0 conda-forge
r-selectr 0.4_2 r40hc72bb7e_1 conda-forge
r-stringi 1.5.3 r40hca8494e_0 conda-forge
r-stringr 1.4.0 r40hc72bb7e_2 conda-forge
r-sys 3.4 r40hcfec24a_0 conda-forge
r-testthat 3.1.1 r40h03ef668_0 conda-forge
r-tibble 3.1.6 r40hcfec24a_0 conda-forge
r-tidyr 1.1.4 r40h03ef668_0 conda-forge
r-tidyselect 1.1.1 r40hc72bb7e_0 conda-forge
r-tidyverse 1.3.1 r40hc72bb7e_0 conda-forge
r-tinytex 0.35 r40hc72bb7e_0 conda-forge
r-tzdb 0.2.0 r40h03ef668_0 conda-forge
r-utf8 1.2.2 r40hcfec24a_0 conda-forge
r-uuid 1.0_3 r40hcfec24a_0 conda-forge
r-vctrs 0.3.8 r40hcfec24a_1 conda-forge
r-viridislite 0.4.0 r40hc72bb7e_0 conda-forge
r-vroom 1.5.7 r40h03ef668_0 conda-forge
r-waldo 0.3.1 r40hc72bb7e_0 conda-forge
r-withr 2.4.3 r40hc72bb7e_0 conda-forge
r-xfun 0.28 r40h03ef668_0 conda-forge
r-xml2 1.3.3 r40h03ef668_0 conda-forge
r-yaml 2.2.1 r40hcfec24a_1 conda-forge
ratelimiter 1.2.0 py_1002 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
reproc 14.2.3 h7f98852_0 conda-forge
reproc-cpp 14.2.3 h9c3ff4c_0 conda-forge
requests 2.26.0 pyhd8ed1ab_1 conda-forge
ruamel_yaml 0.15.80 py36h8f6f2f9_1004 conda-forge
samtools 1.12 h9aed4be_1 bioconda
scikit-learn 0.19.2 py36_blas_openblasha84fab4_201 [blas_openblas] conda-forge
scipy 1.5.3 py36h81d768a_1 conda-forge
seaborn 0.11.2 hd8ed1ab_0 conda-forge
seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 58.0.4 py36h5fab9bb_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 3.0.5 pyh44b312d_0 conda-forge
snakemake-minimal 5.10.0 py_0 bioconda
spades 3.13.0 0 bioconda
sqlite 3.37.0 h9cd32fc_0 conda-forge
sqlparse 0.4.2 pyhd8ed1ab_0 conda-forge
statsmodels 0.12.2 py36he33b4a0_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tabulate 0.8.9 pyhd8ed1ab_0 conda-forge
tbb 2020.2 h4bd325d_4 conda-forge
tk 8.6.11 h27826a3_1 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toposort 1.7 pyhd8ed1ab_0 conda-forge
tornado 6.1 py36h8f6f2f9_1 conda-forge
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
traitlets 4.3.3 pyhd8ed1ab_2 conda-forge
trimal 1.4.1 h7d875b9_5 bioconda
trnascan-se 2.0.9 pl5262h779adbc_1 bioconda
typing_extensions 4.0.1 pyha770c72_0 conda-forge
urllib3 1.26.7 pyhd8ed1ab_0 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
wrapt 1.13.1 py36h8f6f2f9_0 conda-forge
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-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
yaml 0.2.5 h516909a_0 conda-forge
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.4.9 ha95c52a_0 conda-forgeThank you for your time!
meren
commented
2 years ago Hey @Laura-Alex, the only appropriate way to install anvi'o is to follow the anvi'o installation instructions. They are here:
Laura-Alex
commented
2 years ago Thank you. As mentioned in my first post, installing anvi'o in the 'proper' way didn't work for me due to conflicts appearing / environment not solving for r packages.
meren
commented
2 years ago Ah, sorry, @Laura-Alex, I completely missed that part of your first message!
Regardless. There is no other 'official' way to install anvi'o at this point. You can skip installing the R packages, and solve those dependencies if/when the time comes in different ways (by for instance installing them through R directly, rather than through their conda packages).
Best,
Laura-Alex
commented
2 years ago Thank you, I tried installing packages in a different order and that seemed to help things!
Short description of the problem
anvi-self-test --suite minifails when starting the interactive interface; django is blamedanvi'o version
6.2
System info
I have tried to install anvi'o on a computer cluster (CentOS Linux 7 (Core)) in a conda environment.
The original instructions on https://merenlab.org/2016/06/26/installation-v2/ didn't work for me (r-based packages would either get stuck at the Solving Environment part, or just fail with many conflicts). What worked best for me was suggested in the comments:
mamba install -y -c conda-forge -c bioconda anvio==6.2As this is remote work, I have also tried to follow the instructions on https://merenlab.org/2018/03/07/working-with-remote-interative/ . The tests for the remote part seemed to work (
python -c "import webbrowser; webbrowser.open_new('https://www.google.com/')"did outputOPEN_ON_LOCAL[https://www.google.com/], andecho $ANVIO_PORTresults in8090as set.However, I'm not as confident about the local part since it's not something I'm familiar with (only installed Git today for the bash). I've tried to create an alias, and set Chrome as the default browser. I had to create the ~/.ssh directory for the run_webbrowser.py file (maybe Git bash uses a different ~ than is normally used?)
Detailed description of the issue
anvi-self-test --suite miniruns fine up to starting the interactive part of the application. The error message is as follows:Certainly, the django module appears to be the issue, but I've ran
conda listand it appears to be installed. I've also tried to install it again with conda but that did not change the results.Output of
conda list:Help would be much appreciated!