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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Issue in "phyluce_assembly_get_match_counts" #274

Closed claudiavaga closed 2 years ago

claudiavaga commented 2 years ago

Hello!

I am getting an error running the program "phyluce_assembly_get_match_counts"

This is what I am getting:

phyluce_assembly_get_match_counts \

--locus-db /home/geninfo/cvaga/assemblies/uce-search-todas/probe.matches.sqlite \ --taxon-list-config /home/geninfo/cvaga/assemblies/taxon-set-todas.conf \ --taxon-group 'all' \ --incomplete-matrix \ --output /home/geninfo/cvaga/assemblies/taxon-sets-todas/all/all-taxa-incomplete.conf \ --log-path /home/geninfo/cvaga/assemblies/log_todas

2022-04-30 16:20:12,659 - phyluce_assembly_get_match_counts - INFO - =========== Starting phyluce_assembly_get_match_counts ========== 2022-04-30 16:20:12,660 - phyluce_assembly_get_match_counts - INFO - Version: git fatal: Not a git repository: '/home/geninfo/cvaga/.conda/envs/phyluce/lib/python2.7/site-packages/.git' 2022-04-30 16:20:12,660 - phyluce_assembly_get_match_counts - INFO - Argument --extend_locus_db: None 2022-04-30 16:20:12,660 - phyluce_assembly_get_match_counts - INFO - Argument --incomplete_matrix: True 2022-04-30 16:20:12,660 - phyluce_assembly_get_match_counts - INFO - Argument --keep_counts: False 2022-04-30 16:20:12,660 - phyluce_assembly_get_match_counts - INFO - Argument --locus_db: /home/geninfo/cvaga/assemblies/uce-search-todas/probe.matches.sqlite 2022-04-30 16:20:12,661 - phyluce_assembly_get_match_counts - INFO - Argument --log_path: /home/geninfo/cvaga/assemblies/log_todas 2022-04-30 16:20:12,661 - phyluce_assembly_get_match_counts - INFO - Argument --optimize: False 2022-04-30 16:20:12,661 - phyluce_assembly_get_match_counts - INFO - Argument --output: /home/geninfo/cvaga/assemblies/taxon-sets-todas/all/all-taxa-incomplete.conf 2022-04-30 16:20:12,661 - phyluce_assembly_get_match_counts - INFO - Argument --random: False 2022-04-30 16:20:12,661 - phyluce_assembly_get_match_counts - INFO - Argument --sample_size: 10 2022-04-30 16:20:12,662 - phyluce_assembly_get_match_counts - INFO - Argument --samples: 10 2022-04-30 16:20:12,662 - phyluce_assembly_get_match_counts - INFO - Argument --silent: False 2022-04-30 16:20:12,662 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_group: all 2022-04-30 16:20:12,662 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_list_config: /home/geninfo/cvaga/assemblies/taxon-set-todas.conf 2022-04-30 16:20:12,662 - phyluce_assembly_get_match_counts - INFO - Argument --verbosity: INFO 2022-04-30 16:20:12,666 - phyluce_assembly_get_match_counts - INFO - There are 243 taxa in the taxon-group '[all]' in the config file taxon-set-todas.conf 2022-04-30 16:20:12,667 - phyluce_assembly_get_match_counts - INFO - Getting UCE names from database 2022-04-30 16:20:12,671 - phyluce_assembly_get_match_counts - INFO - There are 2490 total UCE loci in the database Traceback (most recent call last): File "/home/geninfo/cvaga/.conda/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 351, in main() File "/home/geninfo/cvaga/.conda/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 339, in main shared_uces = dont_sample_match_groups(log, args, c, organisms, uces) File "/home/geninfo/cvaga/.conda/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 286, in dont_sample_match_groups organismal_matches = get_all_matches_by_organism(c, organisms) File "/home/geninfo/cvaga/.conda/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 161, in get_all_matches_by_organism c.execute("SELECT uce FROM matches WHERE {0} = 1".format(organism)) sqlite3.OperationalError: near "=": syntax error

Do you know what it might be happening? I am attaching also the conf file and the probe.matches.sqlite file!

Thank you in advance for your help!

probe.matches.sqlite-text.txt taxon-set-toda.txt

claudiavaga commented 2 years ago

Found the error! Headers problem:)