Error in "kipoi env create KipoiSplice/4" #623
Comments
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Hi, I am sorry I can not reproduce your errors. Can you please let me know which os you are using? Also: perhaps there is some kind of network issue as I am seeing HTTPSConnection error in the above stack trace. Please provide the stack trace of |
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My OS was CentOS Linux release 7.9.2009 (Core) I run the code "kipoi env create KipoiSplice/4 --verbose". All results are as follow: From https://github.com/kipoi/models
During handling of the above exception, another exception occurred: Traceback (most recent call last): Installing pip dependencies: ...working... Ran pip subprocess with arguments: failed CondaEnvException: Pip failed Traceback (most recent call last): |
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Sorry I dont have access to this particular os. From the stacktrace it seems you have trouble downloading scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl. scikit-learn0.22.2post1 is required to run KipoiSplice/4. Is it possible for you to use a docker or a singularity container? For information about how to use the docker container please check the docker tab here. For singularity, try: This will produce a .sif file which you can use with singularity exec. Let me know. |
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I try used the docker to run kipoisplice. I install docker and get the docker image by run "docker pull haimasree/kipoi-docker:kipoisplice". I creat the directionary by the code "mkdir -p $PWD/kipoi-example". It return "fatal: unable to access 'https://github.com/kipoi/models.git/': gnutls_handshake() failed: The TLS connection was non-properly terminated. |
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Unfortunately I cannot reproduce this error either but I have a few things for you to check out
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Perhaps it would be easier to just copy the entire command using the copy button to the right instead of running them line by line? |
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I have one more thought - First create a conda environment with python 3.5 in you system. Now can you try doing the following? |
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Thanks a lot. KipoiSplice/4 is work when I again used CLI method. I not run the code "source activate kipoi-KipoiSplice__4" and directly run "kipoi env install KipoiSplice/4", "kipoi get-example KipoiSplice/4 -o example" and "kipoi predict KipoiSplice/4 --dataloader_args='{"fasta_file": "example/fasta_file", "gtf_file": "example/gtf_file", "num_workers": 1, "vcf_file": "example/vcf_file"}' -o '/tmp/KipoiSplice|4.example_pred.tsv'" |
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Hi, I get anothor issue that hope you kindly provide help. The example vcf was work. But when I run my vcf file using Homo_sapiens_assembly19.fasta and Homo_sapiens.GRCh37.75.gtf. The error was KeyError: "sequence 'HG1287_PATCH' not present". KipoiSplice/4 only used specific reference sequence and gtf? If yes, could you please provide the link of specific reference sequence and gtf for me to download. The follow are detailed error: |
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An example set of files that is compatible with KipoiSplice can be downloaded with Maybe you can verify with these? Any other advice? |
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I can run KipoiSplice/4 using the example set of files. The error was KeyError: "sequence 'HG1287_PATCH' not present" is exist when I use Homo_sapiens.GRCh37.75.gtf and Homo_sapiens_assembly19.fasta. I find "HG1287_PATCH" is present in Homo_sapiens.GRCh37.75.gtf which might not in Homo_sapiens_assembly19.fasta. There are also many others like HG1287_PATCH in Homo_sapiens.GRCh37.75.gtf. So I just retain information of which the chromosome is 1-22, X and Y in Homo_sapiens.GRCh37.75.gtf. |
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I cant reproduce your errors unfortunately. nanoporetech/medaka#193 I did not have much time to go through this in detail but it seemed pysam versions and/or inconsistency between your gtf and fasta files are two most likely culprits. I also noticed your conda environment is using python 3.7 as opposed to 3.5 as specified here. pysam version inside the docker container is 0.15.2. I cant say for certain but an upgraded pysam version may not stay compatible with KipoiSplice. Perhsps check you pysam version as well? Hope this helps. |
When I run "kipoi env create KipoiSplice/4", it return error as follow:
fatal: unable to access 'https://github.com/kipoi/models.git/': Encountered end of file
Pip subprocess error:
DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)",)': /simple/related/
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f8970314080>: Failed to establish a new connection: [Errno 101] Network is unreachable',)': /packages/42/ec/32310181e803f5d22e0dd33eb18924489b2f8d08cf5b6e116a93a6a5d1c6/scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f8970314f28>: Failed to establish a new connection: [Errno 101] Network is unreachable',)': /packages/42/ec/32310181e803f5d22e0dd33eb18924489b2f8d08cf5b6e116a93a6a5d1c6/scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl
WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f89703149b0>: Failed to establish a new connection: [Errno 101] Network is unreachable',)': /packages/42/ec/32310181e803f5d22e0dd33eb18924489b2f8d08cf5b6e116a93a6a5d1c6/scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl
ERROR: Exception:
Traceback (most recent call last):
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
yield
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/urllib3/response.py", line 519, in read
data = self._fp.read(amt) if not fp_closed else b""
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 62, in read
data = self.__fp.read(amt)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/http/client.py", line 448, in read
n = self.readinto(b)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/http/client.py", line 488, in readinto
n = self.fp.readinto(b)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/socket.py", line 576, in readinto
return self._sock.recv_into(b)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/ssl.py", line 937, in recv_into
return self.read(nbytes, buffer)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/ssl.py", line 799, in read
return self._sslobj.read(len, buffer)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/ssl.py", line 583, in read
v = self._sslobj.read(len, buffer)
socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/cli/base_command.py", line 224, in _main
status = self.run(options, args)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/cli/req_command.py", line 180, in wrapper
return func(self, options, args)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/commands/install.py", line 321, in run
reqs, check_supported_wheels=not options.target_dir
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/resolver.py", line 122, in resolve
requirements, max_rounds=try_to_avoid_resolution_too_deep,
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/resolvelib/resolvers.py", line 445, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/resolvelib/resolvers.py", line 339, in resolve
failure_causes = self._attempt_to_pin_criterion(name, criterion)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/resolvelib/resolvers.py", line 207, in _attempt_to_pin_criterion
criteria = self._get_criteria_to_update(candidate)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/resolvelib/resolvers.py", line 198, in _get_criteria_to_update
for r in self._p.get_dependencies(candidate):
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/provider.py", line 172, in get_dependencies
for r in candidate.iter_dependencies(with_requires)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/provider.py", line 171, in
r
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 257, in iter_dependencies
requires = self.dist.requires() if with_requires else ()
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 239, in dist
self._prepare()
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 226, in _prepare
dist = self._prepare_distribution()
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/resolution/resolvelib/candidates.py", line 319, in _prepare_distribution
self._ireq, parallel_builds=True,
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/operations/prepare.py", line 480, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/operations/prepare.py", line 505, in _prepare_linked_requirement
self.download_dir, hashes,
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/operations/prepare.py", line 257, in unpack_url
hashes=hashes,
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/operations/prepare.py", line 130, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/network/download.py", line 163, in call
for chunk in chunks:
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/cli/progress_bars.py", line 168, in iter
for x in it:
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_internal/network/utils.py", line 88, in response_chunks
decode_content=False,
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/urllib3/response.py", line 576, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/urllib3/response.py", line 541, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/contextlib.py", line 77, in exit
self.gen.throw(type, value, traceback)
File "/root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.
CondaEnvException: Pip failed
Traceback (most recent call last):
File "/root/miniconda3/bin/kipoi", line 8, in
sys.exit(main())
File "/root/miniconda3/lib/python3.7/site-packages/kipoi/main.py", line 105, in main
command_fn(args.command, sys.argv[2:])
File "/root/miniconda3/lib/python3.7/site-packages/kipoi/cli/env.py", line 696, in cli_main
command_fn(args.command, raw_args[1:])
File "/root/miniconda3/lib/python3.7/site-packages/kipoi/cli/env.py", line 461, in cli_create
kipoi_conda.create_env_from_file(env_file, use_stdout=args.verbose)
File "/root/miniconda3/lib/python3.7/site-packages/kipoi_conda/utils.py", line 127, in create_env_from_file
return _call_conda(cmd_list, use_stdout=use_stdout, dry_run=dry_run)
File "/root/miniconda3/lib/python3.7/site-packages/kipoi_conda/utils.py", line 196, in _call_conda
return _call_command("conda", extra_args, use_stdout, return_logs_with_stdout, dry_run=dry_run)
File "/root/miniconda3/lib/python3.7/site-packages/kipoi_utils/utils.py", line 78, in _call_command
raise Exception("could not invoke {0} \nreturn code:{1}\nadditional info:{2}".format(cmd_list, return_code, "".join(error_out)))
Exception: could not invoke ['conda', 'env', 'create', '--file', '/tmp/kipoi/envfiles/ccb72598/kipoi-KipoiSplice__4.yaml']
return code:1
additional info:Collecting package metadata (repodata.json): ...working... doneSolving environment: ...working... donePreparing transaction: ...working... doneVerifying transaction: ...working... doneExecuting transaction: ...working... doneInstalling pip dependencies: ...working... Ran pip subprocess with arguments:['/root/miniconda3/envs/kipoi-KipoiSplice__4/bin/python', '-m', 'pip', 'install', '-U', '-r', '/tmp/kipoi/envfiles/ccb72598/condaenv.mhmd1zw0.requirements.txt']Pip subprocess output:Collecting keras==2.2.4 Using cached Keras-2.2.4-py2.py3-none-any.whl (312 kB)Requirement already satisfied: numpy>=1.9.1 in /root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages (from keras==2.2.4->-r /tmp/kipoi/envfiles/ccb72598/condaenv.mhmd1zw0.requirements.txt (line 10)) (1.15.2)Requirement already satisfied: six>=1.9.0 in /root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages (from keras==2.2.4->-r /tmp/kipoi/envfiles/ccb72598/condaenv.mhmd1zw0.requirements.txt (line 10)) (1.16.0)Requirement already satisfied: h5py in /root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages (from keras==2.2.4->-r /tmp/kipoi/envfiles/ccb72598/condaenv.mhmd1zw0.requirements.txt (line 10)) (2.8.0)Collecting kipoi==0.6.30 Using cached kipoi-0.6.30-py3-none-any.whl (101 kB)Requirement already satisfied: pandas>=0.21.0 in /root/miniconda3/envs/kipoi-KipoiSplice__4/lib/python3.5/site-packages (from kipoi==0.6.30->-r /tmp/kipoi/envfiles/ccb72598/condaenv.mhmd1zw0.requirements.txt (line 1)) (0.23.4)Collecting scikit-learn==0.22.2.post1 Downloading scikit_learn-0.22.2.post1-cp35-cp35m-manylinux1_x86_64.whl (7.0 MB)failed
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