Closed dengzq1234 closed 2 years ago
Hi Ziqi,
While installing mOTUs, the database is downloaded (few Gb). So it might be that it's waiting to download that? Could you otherwise try to install through GitHub?
git clone https://github.com/motu-tool/mOTUs.git
cd motus
python setup.py sdist
motus downloadDB
We are also in the process of adding to pip
. It should be done in a few days.
I see! Thanks Alessio!
Hi, I meet the same problem; and I have git clone mOTUs and run python setup.py, here is the error reported:
python setup.py sdist
/home/ubt/miniconda3/lib/python3.9/site-packages/setuptools/dist.py:757: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
warnings.warn(
running sdist
running egg_info
writing motu_profiler.egg-info/PKG-INFO
writing dependency_links to motu_profiler.egg-info/dependency_links.txt
writing entry points to motu_profiler.egg-info/entry_points.txt
writing top-level names to motu_profiler.egg-info/top_level.txt
package init file 'motus/__init__.py' not found (or not a regular file)
reading manifest file 'motu_profiler.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'motu_profiler.egg-info/SOURCES.txt'
running check
creating motu-profiler-3.0.3
creating motu-profiler-3.0.3/motu_profiler.egg-info
creating motu-profiler-3.0.3/motus
copying files to motu-profiler-3.0.3...
copying LICENSE -> motu-profiler-3.0.3
copying README.md -> motu-profiler-3.0.3
copying setup.cfg -> motu-profiler-3.0.3
copying setup.py -> motu-profiler-3.0.3
copying motu_profiler.egg-info/PKG-INFO -> motu-profiler-3.0.3/motu_profiler.egg-info
copying motu_profiler.egg-info/SOURCES.txt -> motu-profiler-3.0.3/motu_profiler.egg-info
copying motu_profiler.egg-info/dependency_links.txt -> motu-profiler-3.0.3/motu_profiler.egg-info
copying motu_profiler.egg-info/entry_points.txt -> motu-profiler-3.0.3/motu_profiler.egg-info
copying motu_profiler.egg-info/top_level.txt -> motu-profiler-3.0.3/motu_profiler.egg-info
copying motus/PEfiltering.py -> motu-profiler-3.0.3/motus
copying motus/UTIL_log.py -> motu-profiler-3.0.3/motus
copying motus/UTIL_log_col.py -> motu-profiler-3.0.3/motus
copying motus/append.py -> motu-profiler-3.0.3/motus
copying motus/convert_long_reads.py -> motu-profiler-3.0.3/motus
copying motus/downloadDB.py -> motu-profiler-3.0.3/motus
copying motus/map_genes_to_mOTUs.py -> motu-profiler-3.0.3/motus
copying motus/map_mOTUs_to_LGs.py -> motu-profiler-3.0.3/motus
copying motus/metaSNV_DistDiv.py -> motu-profiler-3.0.3/motus
copying motus/metaSNV_Filtering_2.0.py -> motu-profiler-3.0.3/motus
copying motus/motu_utilities.py -> motu-profiler-3.0.3/motus
copying motus/motus.py -> motu-profiler-3.0.3/motus
copying motus/msamtools_python.py -> motu-profiler-3.0.3/motus
copying motus/print_CAMI.py -> motu-profiler-3.0.3/motus
copying motus/runBWA.py -> motu-profiler-3.0.3/motus
copying motus/runBWA_for_snv.py -> motu-profiler-3.0.3/motus
copying motus/test.py -> motu-profiler-3.0.3/motus
Writing motu-profiler-3.0.3/setup.cfg
Creating tar archive
removing 'motu-profiler-3.0.3' (and everything under it)
motus downloadDB
[E::main] Error: database has not been downloaded. Run setup.py before using the motus profiler
could you help with this ?
Can you try pip install motu-profiler
? What does it says?
just can't run motus
(base) ubuntu@ip-172-31-36-88:~$ pip install motu-profiler
Requirement already satisfied: motu-profiler in ./miniconda3/lib/python3.9/site-packages/motu_profiler-3.0.3-py3.9.egg (3.0.3)
(base) ubuntu@ip-172-31-36-88:~$ motus downloadDB
Command 'motus' not found, did you mean:
command 'lotus' from snap lotus (latest)
command 'motes' from snap motes (6.3.3)
command 'notus' from snap notus (0.5.1)
See 'snap info <snapname>' for additional versions.
Hi Both
You're using pip
inside a conda
environment. So my assumption is that you're using the local installation pip
and not the conda pip
. However you're using the conda python
. So there is a disconnect on where motus
is installed and by that cannot be found by python
. Try to use pip
inside python
by using python -m pip ...
. In this case it would be:
python -m pip install motu-profiler
After many tries, I have finally installed mOTUs. And I found the Version: 2.5.1 is not the latest version 3.*, so how can i update to the latest version?
I guess you installed with conda. You can try:
conda install -c bioconda motus=3.0.3
I guess you installed with conda. You can try:
conda install -c bioconda motus=3.0.3
It works, but i still need to download DB again when runs motus. However motus downloadDB always failed(maybe due to slow network), any solution for this ?
motus downloadDB
------------------------------------------------------------------------------
| SETUP MOTUS TOOL |
------------------------------------------------------------------------------
Download the compressed motus database (~3.5Gb)
8%, 273 MB, 87 KB/s, 3214 seconds passedTraceback (most recent call last):
File "/home/ubt/miniconda3/bin/motus", line 7, in <module>
from motus.motus import main
File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/motus.py", line 77, in <module>
motus.downloadDB.main()
File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/downloadDB.py", line 83, in main
save_f(link_db, db_name)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/downloadDB.py", line 45, in save_f
urllib.request.urlretrieve(url, filename, reporthook)
File "/home/ubt/miniconda3/lib/python3.9/urllib/request.py", line 278, in urlretrieve
raise ContentTooShortError(
urllib.error.ContentTooShortError: <urlopen error retrieval incomplete: got only 286555128 out of 3505108629 bytes>
It seems it is downloading really slow (87 KB/s). I actually had the same problem for the first time 5 days ago (and the download would stop also for me). The database is hosted on zenodo, and apparently sometimes it is very slow.
When I tried again the day after it was downloading at 30 MB/s, and the whole database was downloaded after few minutes. Maybe you can try again in a day? If this keep on happening, we might have to change the location of the database!
It seems it is downloading really slow (87 KB/s). I actually had the same problem for the first time 5 days ago (and the download would stop also for me). The database is hosted on zenodo, and apparently sometimes it is very slow.
When I tried again the day after it was downloading at 30 MB/s, and the whole database was downloaded after few minutes. Maybe you can try again in a day? If this keep on happening, we might have to change the location of the database!
I have tried many times to download DB these two days and all failed. I think it is better to change the location .
I guess you installed with conda. You can try:
conda install -c bioconda motus=3.0.3
It works, but i still need to download DB again when runs motus. However motus downloadDB always failed(maybe due to slow network), any solution for this ?
motus downloadDB ------------------------------------------------------------------------------ | SETUP MOTUS TOOL | ------------------------------------------------------------------------------ Download the compressed motus database (~3.5Gb) 8%, 273 MB, 87 KB/s, 3214 seconds passedTraceback (most recent call last): File "/home/ubt/miniconda3/bin/motus", line 7, in <module> from motus.motus import main File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/motus.py", line 77, in <module> motus.downloadDB.main() File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/downloadDB.py", line 83, in main save_f(link_db, db_name) File "/home/ubt/miniconda3/lib/python3.9/site-packages/motus/downloadDB.py", line 45, in save_f urllib.request.urlretrieve(url, filename, reporthook) File "/home/ubt/miniconda3/lib/python3.9/urllib/request.py", line 278, in urlretrieve raise ContentTooShortError( urllib.error.ContentTooShortError: <urlopen error retrieval incomplete: got only 286555128 out of 3505108629 bytes>
I thought i have download motus3 until i saw "Version 2.6.0" when i run motus, though the motus script is under the motus-3.0.3 folder:
python /home/ubt/miniconda3/pkgs/motus-3.0.3-pyhdfd78af_0/python-scripts/motus
Program: motus - a tool for marker gene-based OTU (mOTU) profiling
Version: 2.6.0
Reference: Milanese et al. Microbial abundance, activity and population genomic profiling with mOTUs2. Nature Communications (2019). doi: 10.1038/s41467-019-08844-4
....
my question is am i running motus3 or motus2.6.0 ?
yes, you have mOTUs 2.6.0. You can check also with motus --version
Which for me returns:
motus 3.0.3 on python 3.7.3
It might be the python version the problem? Which python version are you using?
Mine: python ~/miniconda3/pkgs/motus-3.0.3-pyhdfd78af_0/python-scripts/motus --version motus 2.6.0 on python 3.9.7.
so i still do not have motus3.0.3 ? my install command is conda install -c bioconda motus=3.0.3
how can i get real motus3.0.3 then ?
I'm not sure what it is going wrong, but if you do:
conda create -n motus3 motus=3.0.3
where I get:
The following packages will be downloaded:
package | build
---------------------------|-----------------
libblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcblas-3.9.0 |16_osx64_openblas 13 KB conda-forge
libcxx-14.0.6 | hccf4f1f_0 1.3 MB conda-forge
libgfortran-5.0.0 |10_4_0_h97931a8_25 146 KB conda-forge
libgfortran5-11.3.0 | h082f757_25 1.9 MB conda-forge
liblapack-3.9.0 |16_osx64_openblas 13 KB conda-forge
libnghttp2-1.47.0 | h5aae05b_1 875 KB conda-forge
libopenblas-0.3.21 |openmp_h947e540_2 9.6 MB conda-forge
libssh2-1.10.0 | h47af595_3 222 KB conda-forge
metasnv-1.0.3 | py39h3ddd199_4 126 KB bioconda
motus-3.0.3 | pyhdfd78af_0 78 KB bioconda
numpy-1.23.2 | py39h62c883e_0 6.6 MB conda-forge
openssl-3.0.5 | hb81d4ab_1 2.5 MB conda-forge
pandas-1.4.3 | py39hf72b562_0 11.9 MB conda-forge
pip-22.2.2 | pyhd8ed1ab_0 1.5 MB conda-forge
python-3.9.9 |h38b4d05_0_cpython 12.6 MB conda-forge
pytz-2022.2.1 | pyhd8ed1ab_0 224 KB conda-forge
setuptools-65.3.0 | pyhd8ed1ab_1 782 KB conda-forge
tzdata-2022c | h191b570_0 119 KB conda-forge
xz-5.2.6 | h775f41a_0 233 KB conda-forge
------------------------------------------------------------
Total: 50.7 MB
and here I see motus-3.0.3
in the package list.
After installing you can do conda activate motus3
(sometimes you need to do source activate motus3
) to activate the environment.
And now you will have mOTUs3, which you can run just with motus
(once the env is active).
Mine:
$ conda create -n motus3 motus=3.0.3
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- motus=3.0.3
Current channels:
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Can you try: conda create -c bioconda -n motus3 motus=3.0.3
?
Can you try:
conda create -c bioconda -n motus3 motus=3.0.3
?
An unexpected error has occurred:
$ conda create -c bioconda -n motus3 motus=3.0.3
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/ubt/miniconda3/envs/motus3
added / updated specs:
- motus=3.0.3
The following packages will be downloaded:
package | build
---------------------------|-----------------
bottleneck-1.3.5 | py38h7deecbd_0 115 KB
libdeflate-1.8 | h7f8727e_5 51 KB
mkl-service-2.4.0 | py38h7f8727e_0 59 KB
mkl_fft-1.3.1 | py38hd3c417c_0 180 KB
mkl_random-1.2.2 | py38h51133e4_0 308 KB
numexpr-2.8.3 | py38h807cd23_0 125 KB
numpy-1.23.1 | py38h6c91a56_0 11 KB
numpy-base-1.23.1 | py38ha15fc14_0 5.6 MB
pandas-1.4.3 | py38h6a678d5_0 9.9 MB
pip-22.1.2 | py38h06a4308_0 2.5 MB
pyparsing-3.0.9 | py38h06a4308_0 152 KB
python-3.8.1 | h0371630_1 49.5 MB
setuptools-63.4.1 | py38h06a4308_0 1.1 MB
------------------------------------------------------------
Total: 69.5 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu
blas pkgs/main/linux-64::blas-1.0-mkl
bottleneck pkgs/main/linux-64::bottleneck-1.3.5-py38h7deecbd_0
bwa bioconda/linux-64::bwa-0.7.17-h5bf99c6_8
bzip2 pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
ca-certificates pkgs/main/linux-64::ca-certificates-2022.07.19-h06a4308_0
certifi pkgs/main/linux-64::certifi-2022.6.15-py38h06a4308_0
curl pkgs/main/linux-64::curl-7.69.1-hbc83047_0
htslib bioconda/linux-64::htslib-1.9-h4da6232_3
intel-openmp pkgs/main/linux-64::intel-openmp-2021.4.0-h06a4308_3561
krb5 pkgs/main/linux-64::krb5-1.17.1-h173b8e3_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
libcurl pkgs/main/linux-64::libcurl-7.69.1-h20c2e04_0
libdeflate pkgs/main/linux-64::libdeflate-1.8-h7f8727e_5
libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
libffi pkgs/main/linux-64::libffi-3.2.1-hf484d3e_1007
libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1
libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1
libssh2 pkgs/main/linux-64::libssh2-1.10.0-h8f2d780_0
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1
metasnv bioconda/linux-64::metasnv-1.0.3-h230ddbb_2
mkl pkgs/main/linux-64::mkl-2021.4.0-h06a4308_640
mkl-service pkgs/main/linux-64::mkl-service-2.4.0-py38h7f8727e_0
mkl_fft pkgs/main/linux-64::mkl_fft-1.3.1-py38hd3c417c_0
mkl_random pkgs/main/linux-64::mkl_random-1.2.2-py38h51133e4_0
motus bioconda/noarch::motus-3.0.3-pyhdfd78af_0
ncurses pkgs/main/linux-64::ncurses-6.1-he6710b0_1
numexpr pkgs/main/linux-64::numexpr-2.8.3-py38h807cd23_0
numpy pkgs/main/linux-64::numpy-1.23.1-py38h6c91a56_0
numpy-base pkgs/main/linux-64::numpy-base-1.23.1-py38ha15fc14_0
openssl pkgs/main/linux-64::openssl-1.1.1q-h7f8727e_0
packaging pkgs/main/noarch::packaging-21.3-pyhd3eb1b0_0
pandas pkgs/main/linux-64::pandas-1.4.3-py38h6a678d5_0
perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0
pip pkgs/main/linux-64::pip-22.1.2-py38h06a4308_0
pyparsing pkgs/main/linux-64::pyparsing-3.0.9-py38h06a4308_0
python pkgs/main/linux-64::python-3.8.1-h0371630_1
python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0
pytz pkgs/main/linux-64::pytz-2022.1-py38h06a4308_0
readline pkgs/main/linux-64::readline-7.0-h7b6447c_5
samtools bioconda/linux-64::samtools-1.9-h10a08f8_12
setuptools pkgs/main/linux-64::setuptools-63.4.1-py38h06a4308_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sqlite pkgs/main/linux-64::sqlite-3.31.1-h7b6447c_0
tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7f8727e_1
zlib pkgs/main/linux-64::zlib-1.2.12-h7f8727e_2
Proceed ([y]/n)? y
Downloading and Extracting Packages
mkl_random-1.2.2 | 308 KB | ################################################################################################# | 100%
numexpr-2.8.3 | 125 KB | ################################################################################################# | 100%
mkl_fft-1.3.1 | 180 KB | ################################################################################################# | 100%
pip-22.1.2 | 2.5 MB | ################################################################################################# | 100%
bottleneck-1.3.5 | 115 KB | ################################################################################################# | 100%
libdeflate-1.8 | 51 KB | ################################################################################################# | 100%
pandas-1.4.3 | 9.9 MB | ################################################################################################# | 100%
pyparsing-3.0.9 | 152 KB | ################################################################################################# | 100%
python-3.8.1 | 49.5 MB | ################################################################################################# | 100%
numpy-1.23.1 | 11 KB | ################################################################################################# | 100%
setuptools-63.4.1 | 1.1 MB | ################################################################################################# | 100%
numpy-base-1.23.1 | 5.6 MB | ################################################################################################# | 100%
mkl-service-2.4.0 | 59 KB | ################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate motus3
#
# To deactivate an active environment, use
#
# $ conda deactivate
Retrieving notices: ...working... failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 699, in urlopen
httplib_response = self._make_request(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 382, in _make_request
self._validate_conn(conn)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn
conn.connect()
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connection.py", line 411, in connect
self.sock = ssl_wrap_socket(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "/home/ubt/miniconda3/lib/python3.9/ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "/home/ubt/miniconda3/lib/python3.9/ssl.py", line 1040, in _create
self.do_handshake()
File "/home/ubt/miniconda3/lib/python3.9/ssl.py", line 1309, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ubt/miniconda3/lib/python3.9/site-packages/requests/adapters.py", line 439, in send
resp = conn.urlopen(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 783, in urlopen
return self.urlopen(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/connectionpool.py", line 755, in urlopen
retries = retries.increment(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/urllib3/util/retry.py", line 574, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /bioconda/notices.json (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1125, in __call__
return func(*args, **kwargs)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/cli/main.py", line 86, in main_subshell
exit_code = do_call(args, p)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/cli/conda_argparse.py", line 93, in do_call
return getattr(module, func_name)(args, parser)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/core.py", line 75, in wrapper
display_notices(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/core.py", line 39, in display_notices
channel_notice_responses = http.get_notice_responses(channel_name_urls, silent=silent)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/http.py", line 36, in get_notice_responses
return tuple(
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/http.py", line 39, in <genexpr>
(
File "/home/ubt/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 608, in result_iterator
yield fs.pop().result()
File "/home/ubt/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 445, in result
return self.__get_result()
File "/home/ubt/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 390, in __get_result
raise self._exception
File "/home/ubt/miniconda3/lib/python3.9/concurrent/futures/thread.py", line 52, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/http.py", line 42, in <lambda>
lambda args: get_channel_notice_response(*args), url_and_names
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/cache.py", line 37, in wrapper
return_value = func(url, name)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/conda/notices/http.py", line 58, in get_channel_notice_response
resp = session.get(url, allow_redirects=False, timeout=5) # timeout: connect, read
File "/home/ubt/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "/home/ubt/miniconda3/lib/python3.9/site-packages/requests/adapters.py", line 514, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='conda.anaconda.org', port=443): Max retries exceeded with url: /bioconda/notices.json (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1129)')))
`$ /home/ubt/miniconda3/bin/conda create -c bioconda -n motus3 motus=3.0.3`
environment variables:
CIO_TEST=<not set>
CONDA_BACKUP_JAVA_HOME=:-
CONDA_BACKUP_JAVA_LD_LIBRARY_PATH=:-
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/ubt/miniconda3/bin/conda
CONDA_PREFIX=/home/ubt/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/ubt/miniconda3/bin/python
CONDA_ROOT=/home/ubt/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
JAVA_LD_LIBRARY_PATH=/home/ubt/miniconda3/lib/server
PATH=/home/ubt/miniconda3/bin:/home/ubt/work1/tools/lemmi-v2/workflow/scrip
ts:/home/ubt/miniconda3/bin:/home/ubt/miniconda3/condabin:/home/ubt/bi
n:/mnt/sda/tools/emsdk:/mnt/sda/tools/emsdk/upstream/emscripten:/mnt/s
da/tools/emsdk/node/14.18.2_64bit/bin:/usr/local/sbin:/usr/local/bin:/
usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/ho
me/ubt/.local/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /home/ubt/miniconda3
shell level : 1
user config file : /home/ubt/.condarc
populated config files : /home/ubt/.condarc
conda version : 4.14.0
conda-build version : not installed
python version : 3.9.7.final.0
virtual packages : __linux=5.13.0=0
__glibc=2.34=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/ubt/miniconda3 (writable)
conda av data dir : /home/ubt/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/ubt/miniconda3/pkgs
/home/ubt/.conda/pkgs
envs directories : /home/ubt/miniconda3/envs
/home/ubt/.conda/envs
platform : linux-64
user-agent : conda/4.14.0 requests/2.25.1 CPython/3.9.7 Linux/5.13.0-52-generic ubuntu/21.10 glibc/2.34
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]:
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I'm not sure what is happening there. But, since you have a working mOTUs 2.6 version, you can download a database (with mOTUs version 3) that I prepared for you in https://sunagawalab.ethz.ch/share/TEMP_MOTUS_DB/.
You can download with:
wget https://sunagawalab.ethz.ch/share/TEMP_MOTUS_DB/motus-db_3.0.2.tar.gz
and unzip with:
tar -xvzf motus-db_3.0.2.tar.gz
Then you should be able to run it with:
python /home/ubt/miniconda3/pkgs/motus-3.0.3-pyhdfd78af_0/python-scripts/motus -db /path/to/the/downloaded/db/
where you should replace /path/to/the/downloaded/db/
with the database repository that you just unzipped.
I have already downloaded motus-db_3.0.1.tar.gz previously, I am just not sure if mOTUs 2.6 and mOTUs 3 will produce the same results if the database is the same?
There were only minor changes between mOTUs 2.6 and mOTUs 3.0. The naming of the mOTUs changed, and the taxonomy improved with version 3.0.1. But for 3.0.1 and 3.0.2 and 3.0.3 the results are the same.
So if you have mOTUs 2.6, you can use the database from 3.0.1 to run mOTUs.
Hi, I tried to install motus via conda using the follwing command according to the tutorial
conda install -c bioconda motus
but the install process stucked at the Executing transaction for a very long time so I have to stop it, and report showedERROR conda.core.link:_execute(701): An error occurred while installing package 'bioconda::motus-2.1.1-py37_3'.
I tried different motus and python versions and cross platforms but same error occured.
Thanks