ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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urllib.error.URLError: <urlopen error [Errno -2] Name or service not known> #899

Open HFzzzzzzz opened 1 year ago

HFzzzzzzz commented 1 year ago

I tried new methods on a slurm cluster, specifically I download cactus-bin-legacy-v2.4.0.tar.gz Then follow the docs tar -xzf "cactus-bin-${REL_TAG}.tar.gz" cd "cactus-bin-${REL_TAG}" virtualenv -p python3.8 cactus_env echo "export PATH=$(pwd)/bin:\$PATH" >> cactus_env/bin/activate echo "export PYTHONPATH=$(pwd)/lib:\$PYTHONPATH" >> cactus_env/bin/activate source cactus_env/bin/activate python3 -m pip install -U setuptools pip==21.3.1 python3 -m pip install -U -r ./toil-requirement.txt python3 -m pip install -U . cd bin && for i in wigToBigWig faToTwoBit bedToBigBed bigBedToBed bedSort hgGcPercent; do wget -q http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/${i}; chmod ugo+x ${i} ; done , the following problem arises. [2023-01-11T21:50:35+0800] [MainThread] [I] [toil.statsAndLogging] Cactus Command: /home/xuql/cactus-bin-v2.4.0/cactus_env/bin/cactus ./jobstore ./examples/evolverMammals.txt ./evolverMammals.hal --binariesMode local --disableChaining --consCores 50 --maxCores 50 --realTimeLogging --batchSystem slurm [2023-01-11T21:50:35+0800] [MainThread] [I] [toil.statsAndLogging] Cactus Commit: 47f9079cc31a5533ffb76f038480fdec1b6f7c4f [2023-01-11T21:50:35+0800] [MainThread] [I] [toil.statsAndLogging] Tree: ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0; [2023-01-11T21:50:35+0800] [MainThread] [I] [toil.statsAndLogging] Importing https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/evolver/mammals/loci1/simCow.chr6 Traceback (most recent call last): File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 1354, in do_open h.request(req.get_method(), req.selector, req.data, headers, File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 1256, in request self._send_request(method, url, body, headers, encode_chunked) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 1302, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 1251, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 1011, in _send_output self.send(msg) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 951, in send self.connect() File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 1418, in connect super().connect() File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/http/client.py", line 922, in connect self.sock = self._create_connection( File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/socket.py", line 787, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/socket.py", line 918, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno -2] Name or service not known

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/xuql/cactus-bin-v2.4.0/cactus_env/bin/cactus", line 8, in sys.exit(main()) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/cactus/progressive/cactus_progressive.py", line 394, in main input_seq_id_map[genome] = toil.importFile(seq) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/lib/compatibility.py", line 12, in call return func(*args, *kwargs) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/common.py", line 1215, in importFile return self.import_file(srcUrl, sharedFileName, symlink) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/common.py", line 1241, in import_file return self._jobStore.import_file(src_uri, shared_file_name=shared_file_name, symlink=symlink) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/jobStores/abstractJobStore.py", line 423, in import_file return self._import_file(otherCls, File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/jobStores/fileJobStore.py", line 322, in _import_file return super()._import_file(otherCls, uri, shared_file_name=shared_file_name) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/jobStores/abstractJobStore.py", line 453, in _import_file size, executable = otherCls._read_from_url(uri, writable) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/lib/retry.py", line 292, in call return func(args, *kwargs) File "/home/xuql/cactus-bin-v2.4.0/cactus_env/lib/python3.8/site-packages/toil/jobStores/abstractJobStore.py", line 1686, in _read_from_url with closing(urlopen(url.geturl())) as readable: File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 525, in open response = self._open(req, data) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 542, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 502, in _call_chain result = func(args) File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 1397, in https_open return self.do_open(http.client.HTTPSConnection, req, File "/home/xuql/miniconda3/envs/pyhton3.8/lib/python3.8/urllib/request.py", line 1357, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno -2] Name or service not known>

What is the reason for this?

glennhickey commented 1 year ago

It is failing to import one of the test files

[2023-01-11T21:50:35+0800] [MainThread] [I] [toil.statsAndLogging] Importing https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/evolver/mammals/loci1/simCow.chr6

The link works for me now -- so you'll have to verify your internet connection. A good test would be to see if wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactusTestData/master/evolver/mammals/loci1/simCow.chr6 works.