From an HGVSg I try to get the normalized HGVSg, HGVSc and HGVSp via mutalyzer/json/runMutalyzerLight.
On the main instance of mutalyzer no problem. On a local instance I have several problems.
When using the web interface or the JSON API I have two problems:
My variants are located on exonic, intronic or intergenic sequences. In this configuration, mutalyser needs sequences for the normalization. So, it automatically downloads the NC from the EBI into its cache. However, after downloading the NC sequence, it appears to download all transcripts and it fails. This error is probably due to the number of requests. I tried with an EBI API key and the result is the same. I only succeeded for a small chromosome.
127.0.0.1 - - [15/Oct/2019 16:17:36] "GET /name-checker?description=NC_000005.10%3Ag.83538811T%3EC HTTP/1.1" 500 -
Traceback (most recent call last):
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 2463, in __call__
return self.wsgi_app(environ, start_response)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 2449, in wsgi_app
response = self.handle_exception(e)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 1866, in handle_exception
reraise(exc_type, exc_value, tb)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 2446, in wsgi_app
response = self.full_dispatch_request()
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 1951, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 1820, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 1949, in full_dispatch_request
rv = self.dispatch_request()
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/flask/app.py", line 1935, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/website/views.py", line 248, in name_checker
variantchecker.check_variant(description, output)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/variantchecker.py", line 1798, in check_variant
retrieved_record = retriever.loadrecord(record_id)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/Retriever.py", line 661, in loadrecord
filename = self.fetch(accession)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/Retriever.py", line 297, in fetch
retmode='text')
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 195, in efetch
return _open(cgi, variables, post=post)
File "/home/user/Documents/mutalyzer/mutalyzer_env/lib/python2.7/site-packages/Bio/Entrez/__init__.py", line 566, in _open
and exception.status // 100 == 4:
AttributeError: 'HTTPError' object has no attribute 'status'
127.0.0.1 - - [15/Oct/2019 16:17:36] "GET /name-checker?__debugger__=yes&cmd=resource&f=debugger.js HTTP/1.1" 200 -
127.0.0.1 - - [15/Oct/2019 16:17:36] "GET /name-checker?__debugger__=yes&cmd=resource&f=style.css HTTP/1.1" 200 -
127.0.0.1 - - [15/Oct/2019 16:17:36] "GET /name-checker?__debugger__=yes&cmd=resource&f=jquery.js HTTP/1.1" 200 -
127.0.0.1 - - [15/Oct/2019 16:17:37] "GET /name-checker?__debugger__=yes&cmd=resource&f=console.png HTTP/1.1" 200 -
127.0.0.1 - - [15/Oct/2019 16:17:37] "GET /name-checker?__debugger__=yes&cmd=resource&f=console.png HTTP/1.1" 200 -
To get around this problem, I tried to synchronize the cache with the main instance of mutalyzer: mutalyzer-admin sync-cache 'https://mutalyzer.nl/services/?wsdl' 'https://mutalyzer.nl/Reference/{file}'. But this command fails because it inserts data without a "source" when this field cannot be null in the database.
(mutalyzer_env) user@computer:~/Documents/mutalyzer$ mutalyzer-admin sync-cache 'https://mutalyzer.nl/services/?wsdl' 'https://mutalyzer.nl/Reference/{file}'
Traceback (most recent call last):
File "/home/user/Documents/mutalyzer/mutalyzer_env/bin/mutalyzer-admin", line 11, in <module>
load_entry_point('mutalyzer==2.0.31', 'console_scripts', 'mutalyzer-admin')()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/entrypoints/admin.py", line 441, in main
args.func(**{k: v for k, v in vars(args).items()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/entrypoints/admin.py", line 172, in sync_cache
history)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/mutalyzer-2.0.31-py2.7.egg/mutalyzer/sync.py", line 184, in sync_with_remote
session.commit()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 162, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 1027, in commit
self.transaction.commit()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 494, in commit
self._prepare_impl()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 473, in _prepare_impl
self.session.flush()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2459, in flush
self._flush(objects)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2597, in _flush
transaction.rollback(_capture_exception=True)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2557, in _flush
flush_context.execute()
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute
rec.execute(self)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute
uow,
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 245, in save_obj
insert,
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 1138, in _emit_insert_statements
statement, params
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute
return meth(self, multiparams, params)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement
distilled_params,
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context
e, statement, parameters, cursor, context
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1466, in _handle_dbapi_exception
util.raise_from_cause(sqlalchemy_exception, exc_info)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 398, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context
cursor, statement, parameters, context
File "/home/user/Documents/mutalyzer/mutalyzer_env/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 552, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (psycopg2.errors.NotNullViolation) null value in column "source" violates not-null constraint
DETAIL: Failing row contains (24, NM_001286191.2, a9ca5136d888c39876dd0dd95c60dac1, null, null, 2019-10-15 16:13:02.206861).
[SQL: INSERT INTO "references" (accession, checksum, source, source_data, added) VALUES (%(accession)s, %(checksum)s, %(source)s, %(source_data)s, %(added)s) RETURNING "references".id]
[parameters: {'source': None, 'source_data': None, 'added': datetime.datetime(2019, 10, 15, 16, 13, 2, 206861), 'accession': NM_001286191.2, 'checksum': a9ca5136d888c39876dd0dd95c60dac1}]
(Background on this error at: http://sqlalche.me/e/gkpj)
For the installation I followed the instructions on https://mutalyzer.readthedocs.io. I installed version v2.0.31 and the data for the GRCh38 assembly.
How can I load all the necessary information to normalize my data on my local instance? Am I wrong in the way I do it?
Hello,
From an HGVSg I try to get the normalized HGVSg, HGVSc and HGVSp via mutalyzer/json/runMutalyzerLight. On the main instance of mutalyzer no problem. On a local instance I have several problems. When using the web interface or the JSON API I have two problems:
My variants are located on exonic, intronic or intergenic sequences. In this configuration, mutalyser needs sequences for the normalization. So, it automatically downloads the NC from the EBI into its cache. However, after downloading the NC sequence, it appears to download all transcripts and it fails. This error is probably due to the number of requests. I tried with an EBI API key and the result is the same. I only succeeded for a small chromosome.
To get around this problem, I tried to synchronize the cache with the main instance of mutalyzer:
mutalyzer-admin sync-cache 'https://mutalyzer.nl/services/?wsdl' 'https://mutalyzer.nl/Reference/{file}'. But this command fails because it inserts data without a "source" when this field cannot be null in the database.For the installation I followed the instructions on https://mutalyzer.readthedocs.io. I installed version v2.0.31 and the data for the GRCh38 assembly.
How can I load all the necessary information to normalize my data on my local instance? Am I wrong in the way I do it?
Thanks in advance