openpaul
commented
3 years ago NCBI database not present yet (first time used?)
it seems your ete3 installation has not been used before. Please run
eukcc ncbi_updateOr run python and setup ete3 as mentioned here: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html
And try again.
For the conda install, you will need to install pplacer (https://anaconda.org/bioconda/pplacer) using conda as guppy is installed this way.
I hope that helps you get eukcc started.
389419784
Hello,
I try to use eukcc to run my eukaryotic bins, but I can't run normally after installation. How can I solve it?
Using the recommended installation method, use get eukcc quickly by fetching the container as follows: export EUKCC2_DB=/public/home/liqm_1/zhanghx/EukCC/eukcc2_db_ver_1 singularity exec /public/home/liqm_1/zhanghx/EukCC/eukcc2.simg eukcc single --out /public/home/liqm_1/zhanghx/WDNA/eukcc/output --threads 40 /public/home/liqm_1/zhanghx/WDNA/old/new/euk_contigs.fa
And the error is: 21-07-2021 07:58:01: EukCC version 2.0 RC2 21-07-2021 07:58:01: Found 3 bins 21-07-2021 07:58:03: Faa folder exists, remove if you want to rerun this analsys, will reuse it for now 21-07-2021 07:58:03: Searching for marker genes in base database 21-07-2021 07:58:03: Found 10 marker genes, placing them in the tree using epa-ng NCBI database not present yet (first time used?) Traceback (most recent call last): File "/opt/conda/lib/python3.8/urllib/request.py", line 1354, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/opt/conda/lib/python3.8/http/client.py", line 1255, in request self._send_request(method, url, body, headers, encode_chunked) File "/opt/conda/lib/python3.8/http/client.py", line 1301, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/opt/conda/lib/python3.8/http/client.py", line 1250, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/opt/conda/lib/python3.8/http/client.py", line 1010, in _send_output self.send(msg) File "/opt/conda/lib/python3.8/http/client.py", line 950, in send self.connect() File "/opt/conda/lib/python3.8/http/client.py", line 1417, in connect super().connect() File "/opt/conda/lib/python3.8/http/client.py", line 921, in connect self.sock = self._create_connection( File "/opt/conda/lib/python3.8/socket.py", line 787, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "/opt/conda/lib/python3.8/socket.py", line 918, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno -3] Temporary failure in name resolution During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/conda/bin/eukcc", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/eukcc/main.py", line 408, in main
eukcc_folder(args)
File "/opt/conda/lib/python3.8/site-packages/eukcc/refine.py", line 65, in eukcc_folder
refine(state)
File "/opt/conda/lib/python3.8/site-packages/eukcc/refine.py", line 149, in refine
bins.append(bin(state, wd, path, protein=True))
File "/opt/conda/lib/python3.8/site-packages/eukcc/bin.py", line 23, in init
self.run_eukcc()
File "/opt/conda/lib/python3.8/site-packages/eukcc/bin.py", line 43, in run_eukcc
clade = E.determine_subdb()
File "/opt/conda/lib/python3.8/site-packages/eukcc/eukcc.py", line 359, in determine_subdb
lng = tax_LCA(tree, info, places)
File "/opt/conda/lib/python3.8/site-packages/eukcc/treehandler.py", line 138, in tax_LCA
info = load_tax_info(taxinfo)
File "/opt/conda/lib/python3.8/site-packages/eukcc/base.py", line 55, in load_tax_info
ncbi = NCBITaxa()
File "/opt/conda/lib/python3.8/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 112, in init
self.update_taxonomy_database(taxdump_file)
File "/opt/conda/lib/python3.8/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 131, in update_taxonomy_database
update_db(self.dbfile)
File "/opt/conda/lib/python3.8/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 758, in update_db
(md5filename, ) = urlretrieve("https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.md5")
File "/opt/conda/lib/python3.8/urllib/request.py", line 247, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/opt/conda/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/opt/conda/lib/python3.8/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/opt/conda/lib/python3.8/urllib/request.py", line 542, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/opt/conda/lib/python3.8/urllib/request.py", line 502, in _call_chain
result = func(*args)
File "/opt/conda/lib/python3.8/urllib/request.py", line 1397, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/opt/conda/lib/python3.8/urllib/request.py", line 1357, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -3] Temporary failure in name resolution>
**While I use conda to install, the following error will be reported, and I have installed guppy3 in Python3
eukcc folder --out /public/home/liqm_1/zhanghx/WDNA/INITIAL_BINNING/eukcc --threads 80 --links /public/home/liqm_1/zhanghx/WDNA/INITIAL_BINNING/concoct_linktable.csv /public/home/liqm_1/zhanghx/WDNA/INITIAL_BINNING/concoct_bins 26-07-2021 09:57:49: EukCC version 2.0 26-07-2021 09:57:49: Found 4 bins 26-07-2021 09:57:50: Missing dependencies. Traceback (most recent call last): File "/public/home/liqm_1/software/miniconda3/envs/eukcc/bin/eukcc", line 10, in
sys.exit(main())
File "/public/home/liqm_1/software/miniconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/main.py", line 413, in main
eukcc_folder(args)
File "/public/home/liqm_1/software/miniconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/refine.py", line 65, in eukcc_folder
refine(state)
File "/public/home/liqm_1/software/miniconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/refine.py", line 133, in refine
E = eukcc(state)
File "/public/home/liqm_1/software/miniconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/eukcc.py", line 184, in init
self.check_dependencies()
File "/public/home/liqm_1/software/miniconda3/envs/eukcc/lib/python3.9/site-packages/eukcc/eukcc.py", line 795, in check_dependencies
raise EnvironmentError("Missing dependencies: {}".format(", ".join(missing)))
OSError: Missing dependencies: guppy