error

[handomsu]

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]

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]

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]

are you on NFS?