Please bear with me as I this is all new to me (Sanger background). I have eventually made my way to this step and I continue to get the following error "sqlite3.OperationalError: near "=": syntax error". See the full parallel file below: I am not sure where this error could be, I even reran the match_contigs_to_probes set. Any ideas? Attached are my config and shell script. Additionally I created the "taxon-sets/all" folders in my scratch (work area).
Hello again,
Please bear with me as I this is all new to me (Sanger background). I have eventually made my way to this step and I continue to get the following error "sqlite3.OperationalError: near "=": syntax error". See the full parallel file below: I am not sure where this error could be, I even reran the match_contigs_to_probes set. Any ideas? Attached are my config and shell script. Additionally I created the "taxon-sets/all" folders in my scratch (work area).
Thank you in advance, Jami5on
6_get_match_counts.txt taxon_set.txt
[38;21m2024-04-16 17:00:58,400 - phyluce_assembly_get_match_counts - INFO - =========== Starting phyluce_assembly_get_match_counts ==========[0m [38;21m2024-04-16 17:00:58,434 - phyluce_assembly_get_match_counts - INFO - Version: 1.7.3[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Commit: None[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --extend_locus_db: None[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --incomplete_matrix: True[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --keep_counts: False[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --locus_db: /scratch/jr4253/uce_search_results/probe.matches.sqlite[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --log_path: None[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --optimize: False[0m [38;21m2024-04-16 17:00:58,435 - phyluce_assembly_get_match_counts - INFO - Argument --output: /scratch/jr4253/taxon-sets/all/all_taxa_incomplete.conf[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --random: False[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --sample_size: 10[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --samples: 10[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --silent: False[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_group: all[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_list_config: /scratch/jr4253/taxon_set.conf[0m [38;21m2024-04-16 17:00:58,436 - phyluce_assembly_get_match_counts - INFO - Argument --verbosity: INFO[0m [38;21m2024-04-16 17:00:58,471 - phyluce_assembly_get_match_counts - INFO - There are 38 taxa in the taxon-group '[all]' in the config file taxon_set.conf[0m [38;21m2024-04-16 17:00:58,471 - phyluce_assembly_get_match_counts - INFO - Getting UCE names from database[0m [38;21m2024-04-16 17:00:58,555 - phyluce_assembly_get_match_counts - INFO - There are 2941 total UCE loci in the database[0m Traceback (most recent call last): File "/home/jr4253/.conda/envs/phyluce-1.7.3/bin/phyluce_assembly_get_match_counts", line 409, in
main()
File "/home/jr4253/.conda/envs/phyluce-1.7.3/bin/phyluce_assembly_get_match_counts", line 390, in main
shared_uces = dont_sample_match_groups(log, args, c, organisms, uces)
File "/home/jr4253/.conda/envs/phyluce-1.7.3/bin/phyluce_assembly_get_match_counts", line 315, in dont_sample_match_groups
organismal_matches = get_all_matches_by_organism(c, organisms)
File "/home/jr4253/.conda/envs/phyluce-1.7.3/bin/phyluce_assembly_get_match_counts", line 172, in get_all_matches_by_organism
c.execute("SELECT uce FROM matches WHERE {0} = 1".format(organism))
sqlite3.OperationalError: near "=": syntax error