I am trying to build the sword mode --light database. I already run step1~4, but this error always appears at step 5. Does anyone know how to solve it?
This is my error message:
(microbeannotator) chin@a305-9999:~/chin$ microbeannotator_db_builder -d microbeannotator_swordDB/ -m sword -t 10 --light --step 5 --no_aspera
2023-05-15 17:04:56,229 [INFO]: This is MicrobeAnnotator v2.0.4
2023-05-15 17:04:56,229 [INFO]: I will download and format the databases I use.
2023-05-15 17:04:56,229 [INFO]: Creating database folders
2023-05-15 17:04:56,230 [INFO]: Step 5
2023-05-15 17:04:56,230 [INFO]: Parsing microbeannotator_swordDB/temp_swissprot_dat_files/uniprot_sprot.dat.gz and storing in microbeannotator_swordDB/uniprot_swissprot.table
2023-05-15 17:06:28,890 [INFO]: Finished
2023-05-15 17:06:28,890 [INFO]: Step 12
2023-05-15 17:06:28,890 [INFO]: Merging annotations into SQLite database.
2023-05-15 17:06:28,911 [INFO]: Creating RefSeq table
Traceback (most recent call last):
File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in
main()
File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main
single_step, aspera, keep_temp, bin_path)
File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 231, in database_duilder
sqlite.create_swissprot_table(sql_database, final_sprot_table)
File "/home/public/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/sqlite3_database_builder.py", line 58, in create_swissprot_table
process TEXT, interpro TEXT, pfam TEXT, ec_number TEXT)')
sqlite3.OperationalError: database is locked
I am trying to build the sword mode --light database. I already run step1~4, but this error always appears at step 5. Does anyone know how to solve it?
This is my error message: (microbeannotator) chin@a305-9999:~/chin$ microbeannotator_db_builder -d microbeannotator_swordDB/ -m sword -t 10 --light --step 5 --no_aspera 2023-05-15 17:04:56,229 [INFO]: This is MicrobeAnnotator v2.0.4 2023-05-15 17:04:56,229 [INFO]: I will download and format the databases I use. 2023-05-15 17:04:56,229 [INFO]: Creating database folders 2023-05-15 17:04:56,230 [INFO]: Step 5 2023-05-15 17:04:56,230 [INFO]: Parsing microbeannotator_swordDB/temp_swissprot_dat_files/uniprot_sprot.dat.gz and storing in microbeannotator_swordDB/uniprot_swissprot.table 2023-05-15 17:06:28,890 [INFO]: Finished 2023-05-15 17:06:28,890 [INFO]: Step 12 2023-05-15 17:06:28,890 [INFO]: Merging annotations into SQLite database. 2023-05-15 17:06:28,911 [INFO]: Creating RefSeq table Traceback (most recent call last): File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in
main()
File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main
single_step, aspera, keep_temp, bin_path)
File "/home/public/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 231, in database_duilder
sqlite.create_swissprot_table(sql_database, final_sprot_table)
File "/home/public/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/sqlite3_database_builder.py", line 58, in create_swissprot_table
process TEXT, interpro TEXT, pfam TEXT, ec_number TEXT)')
sqlite3.OperationalError: database is locked