phyluce_assembly_match_contigs_to_probes stopped working

[marianamateos]

I had run successfully phyluce_assembly_match_contigs_to_probes on similar datasets a few days ago. I now get the error message below concerning 3 lines in the "phyluce_assembly_match_contigs_to_probes" (complete paths have been remove). The only thing I might have done between the time when it was working and when it stopped, was install sqlite3 (again).

/miniconda/envs/phyluce-1.7.2/bin/phyluce_assembly_match_contigs_to_probes \ --contigs trinity-assemblies \ --probes hymenoptera-v2-PRINCIPAL-bait-set.fasta.txt \ --output uce-search-results 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - ======= Starting phyluce_assembly_match_contigs_to_probes ======= 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Version: 1.7.2 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Commit: None 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /trinity-assemblies 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --csv: None 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None 2023-03-04 19:56:31,021 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: None 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 80 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 80 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /uce-search-results 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /hymenoptera-v2-PRINCIPAL-bait-set.fasta.txt 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*) 2023-03-04 19:56:31,022 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO 2023-03-04 19:56:31,258 - phyluce_assembly_match_contigs_to_probes - INFO - Creating the UCE-match database Traceback (most recent call last): File "/miniconda/envs/phyluce-1.7.2/bin/phyluce_assembly_match_contigs_to_probes", line 421, in main() File "miniconda/envs/phyluce-1.7.2/bin/phyluce_assembly_match_contigs_to_probes", line 305, in main log, os.path.join(args.output, "probe.matches.sqlite"), organisms, uces File "miniconda/envs/phyluce-1.7.2/bin/phyluce_assembly_match_contigs_to_probes", line 129, in create_probe_database c.execute(query) sqlite3.OperationalError: near ")": syntax error

[spilornis-ng]

Hi were you able to resolve this?? I am still trying to figure this out!