Just be aware that sqlite (sqlite3) does not work with AWS EFS drive.

[spz1st]

I got the following error when I tried the command "python vcf2db.py test.vcf test.ped test.db" at an EFS drive on a cfncluster. It produced an empty db file. But it worked if I tried to produce the db file somewhere else, like "python vcf2db.py test.vcf test.ped ~/test.db".

Traceback (most recent call last): File "vcf2db.py", line 806, in VCFDB(a.VCF, a.db, a.ped, black_list=a.info_exclude, expand=a.expand, blobber=main_blo bber) File "vcf2db.py", line 213, in __init__ self.samples = self.create_samples() File "vcf2db.py", line 534, in create_samples t.create() File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/sql/sch ema.py", line 742, in create checkfirst=checkfirst) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1920, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1529, in _run_visitor **kwargs).traverse_single(element) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/sql/vis itors.py", line 121, in traverse_single return meth(obj, **kw) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/sql/ddl .py", line 767, in visit_table include_foreign_key_constraints=include_foreign_key_constraints File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 945, in execute return meth(self, multiparams, params) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/sql/ddl .py", line 68, in _execute_on_connection return connection._execute_ddl(self, multiparams, params) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1002, in _execute_ddl compiled File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1189, in _execute_context context) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1393, in _handle_dbapi_exception exc_info File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/util/co mpat.py", line 202, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ base.py", line 1182, in _execute_context context) File "/home/centos/miniconda/envs/python2/lib/python2.7/site-packages/sqlalchemy/engine/ default.py", line 469, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) disk I/O error [SQL: u'\nCREAT E TABLE samples (\n\tsample_id INTEGER NOT NULL, \n\tfamily_id VARCHAR(1), \n\tname VARCHA R(5), \n\tpaternal_id VARCHAR(5), \n\tmaternal_id VARCHAR(5), \n\tsex VARCHAR(2), \n\tphen otype VARCHAR(2), \n\textra VARCHAR(3), \n\tPRIMARY KEY (sample_id)\n)\n\n']

[brentp]

Thanks for reporting. closed in #23