Currently, I am running phyluce and trying to match my contigs with designed probes. I have run the particular code (phyluce_assembly_match_contigs_to_probes) several times with my own data and everything works fine, except for now. Everytime, I try to run this piece of code I get the issue 'sqlite3.OperationalError:database is locked'. I have tried to figure out what database is locked, but when I look into sqlite3, there are no databases to be found. Also, I cannot trace any 'hidden locked files' back in any of the directories.
Any help on how to solve this problem would be very much appreciated!
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - ======= Starting phyluce_assembly_match_contigs_to_probes =======
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Version: 1.7.1
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Commit: None
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /USER/SNP_calling/contigs
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --csv: None
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: None
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 85
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 85
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /USER/SNP_calling/uce-search-results
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /USER/SNP_calling/uce-20k-probes.fasta
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*)
2022-01-24 18:23:35,327 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO
2022-01-24 18:23:35,470 - phyluce_assembly_match_contigs_to_probes - INFO - Creating the UCE-match database
Traceback (most recent call last):
File "/home/User/miniconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 421, in <module>
main()
File "/home/User/miniconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 305, in main
log, os.path.join(args.output, "probe.matches.sqlite"), organisms, uces
File "/home/User/miniconda3/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 129, in create_probe_database
c.execute(query)
sqlite3.OperationalError: database is locked```
