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cruizperez / MicrobeAnnotator

Pipeline for metabolic annotation of microbial genomes
Artistic License 2.0
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sqlite3 error #54

Open PengfanZhang opened 2 years ago

PengfanZhang commented 2 years ago

Hi,

I'm runnining microbeannotator with either light or full version, but I'm stuck with the sqlite3 error with the swissprot database.

Traceback (most recent call last):
  File "/netscratch/dep_psl/grp_rgo/pzhang/tools/MicrobeAnnotator/bin/microbeannotator", line 994, in <module>
    main()
  File "/netscratch/dep_psl/grp_rgo/pzhang/tools/MicrobeAnnotator/bin/microbeannotator", line 489, in main
    refdata.microbeannotator_db, "swissprot", significant_hits)
  File "/netscratch/dep_psl/grp_rgo/pzhang/tools/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/sqlite3_search.py", line 135, in search_ids_imported
    cur.execute("SELECT * FROM " + database_table + " WHERE gene_id=?", (gene_id,))
sqlite3.OperationalError: no such table: swissprot

I'm wondering how I can fix it?

jolbi commented 2 years ago

Hi,

I am facing the same error. I builded the database using https://github.com/silvtal/MicrobeAnnotator branch, because I had problems with downloading without Aspera. db_builder finished without errors, but when I look at the db dir, file microbeannotator.db is empty. File conversion.db seems of appropriate size, protein_db dir also looks good.

Which step of the db_builder should I look at to troubleshoot microbeannotator.db creation?

natashagriffin commented 2 years ago

Hi! I just ran into this same error, missing swissprot table and an empty microbeannotator.db file. Did either of you find a solution already? If I figure it out I will update here.

ChingHsiangChin commented 1 year ago

Hi, I am facing a similar error in --light mode at step 12, saying that my database is locked.

Traceback (most recent call last): File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line main() File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line single_step, aspera, keep_temp, bin_path) File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line sqlite.create_swissprot_table(sql_database, final_sprot_table) File "/home/public/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeanno process TEXT, interpro TEXT, pfam TEXT, ec_number TEXT)') sqlite3.OperationalError: database is locked

Any idea how to solve it?