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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
318 stars 120 forks source link

error #920

Open handomsu opened 5 years ago

handomsu commented 5 years ago

gemini load -v sample.raw_variants.vcf -t snpEff my.db CADD scores are being loaded (to skip use:--skip-cadd). GERP per bp is being loaded (to skip use:--skip-gerp-bp). Traceback (most recent call last): File "/raid/gemini/tool/bin/gemini", line 7, in gemini_main.main() File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 1248, in main args.func(parser, args) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_main.py", line 204, in load_fn gemini_load.load(parser, args) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 51, in load l = load_singlecore(args) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load.py", line 85, in load_singlecore l = GeminiLoader(args) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 126, in init self._create_db([x[0] for x in self._extra_effect_fields]) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/gemini_load_chunk.py", line 357, in _create_db self.c, self.metadata = database.create_tables(db_path, effect_fields or [], not self.args.skip_pls) File "/raid/gemini/data/anaconda/lib/python2.7/site-packages/gemini/database.py", line 394, in create_tables e.connect().connection.connection.text_factory = str pysqlite2.dbapi2.ProgrammingError: Cannot operate on a closed database. https://github.com/arq5x/gemini/issues

brentp commented 5 years ago

I would run ls my.db* and ls -a to check for .lock files from a previous run that make sqlite think the database is in use.

handomsu commented 5 years ago

Thank you, but it doesn't work.. ls -a . .. data gemini_install.py my.db sample.raw_variants.vcf tool rm my.db also doesn't work

brentp commented 5 years ago

are you on NFS?