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Creating NCBITaxa database on first run crashes if multithreading #3

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matnguyen opened this issue Aug 10, 2018 · 0 comments
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@matnguyen
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NCBI database not present yet (first time used?)
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
 1832000 generating entries...
Uploading to /home/klw17/.etetoolkit/taxa.sqlite
Traceback (most recent call last):
  File "NGSweep.py", line 220, in <module>
    args.taxon_id)
  File "/projects/pathogist/klw17/NGSweep/src/preprocess.py", line 33, in __init__
    ncbi = NCBITaxa()
  File "/home/klw17/anaconda3/envs/ngsweep/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 110, in __init__
    self.update_taxonomy_database(taxdump_file)
  File "/home/klw17/anaconda3/envs/ngsweep/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
    update_db(self.dbfile)
  File "/home/klw17/anaconda3/envs/ngsweep/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
    upload_data(dbfile)
  File "/home/klw17/anaconda3/envs/ngsweep/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 791, in upload_data
    db.execute(cmd)
sqlite3.OperationalError: database is locked
@matnguyen matnguyen self-assigned this Aug 10, 2018
@matnguyen matnguyen added the bug Something isn't working label Aug 10, 2018
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