New try with conda install and Python 3.7:
conda create -c biobakery -n biobakery_3.7 python=3.7 biobakery_workflows
First try:
biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/bin/vis.py”, line 123, in
args.introduction_text = “{#id .class width=675px height=505px}\n\n”+intro_methods
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1170, in get_package_file
found_files=list(filter(lambda file: os.path.isfile(os.path.join(package_install_folder,file)),os.listdir(package_install_folder)))
FileNotFoundError: [Errno 2] No such file or directory: ‘/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/biobakery_workflows/…/images’
As before, I did:
ln -s /home/theoscilicium/miniconda3/envs/biobakery_3.7/images /home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/images
Suggestion: fix conda install to avoid this path problem
Second try:
biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 481, in add_archive
output=subprocess.check_output([archive_software,“–help”])
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/subprocess.py”, line 411, in check_output
**kwargs).stdout
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/subprocess.py”, line 488, in run
with Popen(*popenargs, **kwargs) as process:
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/subprocess.py”, line 800, in init
restore_signals, start_new_session)
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/subprocess.py”, line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘zip’: ‘zip’During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/bin/vis.py”, line 214, in
remove_log=True)
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 483, in add_archive
raise EnvironmentError("Unable to archive document with software requested. Please install " +archive_software)
OSError: Unable to archive document with software requested. Please install zip
Problem solved by doing conda install zip. Suggestion: add zip as dependency
Third try:
biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/
(Nov 04 10:15:21) [1/3 - 33.33%] **Skipped ** Task 0: humann_rename_table_ecs
(Nov 04 10:15:21) [1/3 - 33.33%] **Ready ** Task 2: document
(Nov 04 10:15:21) [1/3 - 33.33%] **Started ** Task 2: document
(Nov 04 10:15:21) [2/3 - 66.67%] **Failed ** Task 2: document
(Nov 04 10:15:21) [3/3 - 100.00%] **Failed ** Task 4: archive
Run Finished
Task 2 failed
Name: document
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in _run_task_locally
action_func(task)
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/document.py”, line 232, in create
from pweave import PwebPandocFormatter, Pweb, PwebProcessor
ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’ (/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/pweave/init.py)Task 4 failed
Name: archive
Original error:
Task failed because parent task `2’ failed
Traceback (most recent call last):
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/bin/vis.py”, line 217, in
workflow.go()
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 804, in go
self._handle_finished()
File “/home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 836, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed
So, as of 04/11/2022, the problem described in Sept. 2020 is still not resolved.
EDIT for more info:
return of conda list
packages in environment at /home/theoscilicium/miniconda3/envs/biobakery_3.7:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.7.2 h166bdaf_0 conda-forge
anadama2 0.10.0 pyhb8aa349_0 biobakery
attrs 22.1.0 pyh71513ae_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
biobakery_workflows 3.1 pyh0d95946_0 biobakery
biom-format 2.1.12 py37hda87dfa_1 conda-forge
biopython 1.79 py37h540881e_2 conda-forge
blast 2.13.0 hf3cf87c_0 bioconda
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
bowtie2 2.5.0 py37hb24965f_0 bioconda
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
brotlipy 0.7.0 py37h540881e_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.9.24 ha878542_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2022.9.24 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py37h43b0acd_1 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 py37h89c1867_0 conda-forge
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
cryptography 38.0.2 py37h5994e8b_1 conda-forge
curl 7.86.0 h2283fc2_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
debugpy 1.6.3 py37hd23a5d3_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
dendropy 4.5.2 pyh3252c3a_0 bioconda
diamond 2.0.15 hb97b32f_1 bioconda
entrez-direct 16.2 he881be0_1 bioconda
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
expat 2.5.0 h27087fc_0 conda-forge
fastqc 0.11.9 hdfd78af_1 bioconda
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 2.14.1 hc2a2eb6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 py37h540881e_0 conda-forge
freetype 2.12.1 hca18f0e_0 conda-forge
future 0.18.2 py37h89c1867_5 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glpk 4.57 0 bioconda
graphite2 1.3.13 h58526e2_1001 conda-forge
h5py 3.7.0 nompi_py37hf1ce037_101 conda-forge
harfbuzz 5.3.0 h418a68e_0 conda-forge
hdf5 1.12.2 nompi_h4df4325_100 conda-forge
humann 3.6 pyhdf09c49_0 biobakery
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py37h89c1867_0 conda-forge
importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.16.2 pyh210e3f2_0 conda-forge
ipython 7.33.0 py37h89c1867_0 conda-forge
jedi 0.18.1 py37h89c1867_1 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
jpeg 9e h166bdaf_2 conda-forge
jsonschema 4.17.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.4.4 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py37h89c1867_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
kneaddata 0.12.0 pyhdfd78af_0 bioconda
krb5 1.19.3 h08a2579_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.39 hc81fddc_0 conda-forge
leveldb 0.193 py37h2f20fdb_0 biobakery
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
libbrotlidec 1.0.9 h166bdaf_8 conda-forge
libbrotlienc 1.0.9 h166bdaf_8 conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.86.0 h2283fc2_1 conda-forge
libdeflate 1.6 h516909a_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libglib 2.74.1 h7a41b64_0 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.47.0 hff17c54_1 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.38 h753d276_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.39.4 h753d276_0 conda-forge
libssh2 1.10.0 hf14f497_3 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libtiff 4.2.0 hf544144_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp-base 1.2.4 h166bdaf_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
markdown 3.4.1 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.1 py37h540881e_1 conda-forge
matplotlib-base 3.5.3 py37hf395dca_2 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
metaphlan 3.0 pyh5ca1d4c_1 bioconda
mistune 2.0.4 pyhd8ed1ab_0 conda-forge
msgpack-python 1.0.4 py37h7cecad7_0 conda-forge
munkres 1.0.7 py_1 bioconda
muscle 5.1 h9f5acd7_1 bioconda
nbclient 0.7.0 pyhd8ed1ab_0 conda-forge
nbconvert 7.2.3 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.2.3 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.2.3 pyhd8ed1ab_0 conda-forge
nbformat 5.7.0 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
networkx 2.7.1 pyhd8ed1ab_0 conda-forge
numpy 1.21.6 py37h976b520_0 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjdk 17.0.3 hea3dc9f_3 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 3.0.7 h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pandoc 2.19.2 h32600fe_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.37 hc3806b6_1 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.38 pl5321hdfd78af_4 bioconda
perl-common-sense 3.75 pl5321hdfd78af_0 bioconda
perl-compress-raw-bzip2 2.201 pl5321h87f3376_1 bioconda
perl-compress-raw-zlib 2.105 pl5321h87f3376_0 bioconda
perl-encode 3.19 pl5321hec16e2b_1 bioconda
perl-exporter 5.72 pl5321hdfd78af_2 bioconda
perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda
perl-extutils-makemaker 6.66 0 bioconda
perl-io-compress 2.201 pl5321h87f3376_0 bioconda
perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h9f5acd7_5 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321hec16e2b_1 bioconda
perl-parent 0.236 pl5321hdfd78af_2 bioconda
perl-pathtools 3.75 pl5321hec16e2b_3 bioconda
perl-scalar-list-utils 1.62 pl5321hec16e2b_1 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pexpect 4.8.0 py37hc8dfbb8_1 conda-forge
pickleshare 0.7.5 py37hc8dfbb8_1002 conda-forge
pillow 8.2.0 py37h4600e1f_1 conda-forge
pip 22.3 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.31 pyha770c72_0 conda-forge
psutil 5.9.3 py37h540881e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pweave 0.30.3 py_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.13.0 pyhd8ed1ab_0 conda-forge
pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 py37h540881e_1 conda-forge
pysam 0.16.0 py37ha9a96c6_0 bioconda
pysocks 1.7.1 py37h89c1867_5 conda-forge
python 3.7.12 hf930737_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge
python_abi 3.7 2_cp37m conda-forge
pytz 2022.6 pyhd8ed1ab_0 conda-forge
pyzmq 24.0.1 py37h0c0c2a8_0 conda-forge
raxml 8.2.12 hec16e2b_4 bioconda
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.1 pyhd8ed1ab_1 conda-forge
samtools 0.1.19 h20b1175_10 bioconda
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
setuptools 59.8.0 py37h89c1867_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sqlite 3.39.4 h4ff8645_0 conda-forge
tbb 2021.6.0 h924138e_1 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tornado 6.2 py37h540881e_0 conda-forge
traitlets 5.5.0 pyhd8ed1ab_0 conda-forge
trf 4.09.1 hec16e2b_2 bioconda
trimmomatic 0.39 hdfd78af_2 bioconda
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 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-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 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 5.2.6 h166bdaf_0 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zip 3.0 h7f98852_1 conda-forge
zipp 3.10.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h6239696_4 conda-forge