search

faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
Other
78 stars 49 forks source link

phyluce_assembly_get_match_counts #191

Closed probstrodolfo closed 4 years ago

probstrodolfo commented 4 years ago

Hi Dr. Faircloth, I've been getting the same error message (please see below) when trying to run "phyluce_assembly_get_match_counts". I tried to go around this by setting up a git repository in my wd, with no success. Then I did the same (git init) for the repository accused in the error and I am not sure what is the issue here. Could it be any issue with my HEAD file? Any idea what is causing this? I appreciate any feedback. Thanks, Rodolfo

(phyluce) bus-094542:uce-analysis rprobst$ phyluce_assembly_get_match_counts --locus-db //Users/rprobst/Desktop/uce-analysis/lastz-80-80/probe.matches.sqlite --taxon-list-config datasets.conf --taxon-group 'myrmelachista1' --output /Users/rprobst/Desktop/uce-analysis/taxon-set1/dataset1.conf 2020-05-01 07:19:13,009 - phyluce_assembly_get_match_counts - INFO - =========== Starting phyluce_assembly_get_match_counts ========== 2020-05-01 07:19:13,009 - phyluce_assembly_get_match_counts - INFO - Version: git fatal: not a git repository: '/Users/rprobst/anaconda2/envs/phyluce/lib/python2.7/site-packages/.git' 2020-05-01 07:19:13,009 - phyluce_assembly_get_match_counts - INFO - Argument --extend_locus_db: None 2020-05-01 07:19:13,009 - phyluce_assembly_get_match_counts - INFO - Argument --incomplete_matrix: False 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --keep_counts: False 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --locus_db: //Users/rprobst/Desktop/uce-analysis/lastz-80-80/probe.matches.sqlite 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --log_path: None 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --optimize: False 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --output: /Users/rprobst/Desktop/uce-analysis/taxon-set1/dataset1.conf 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --random: False 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --sample_size: 10 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --samples: 10 2020-05-01 07:19:13,010 - phyluce_assembly_get_match_counts - INFO - Argument --silent: False 2020-05-01 07:19:13,011 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_group: myrmelachista1 2020-05-01 07:19:13,011 - phyluce_assembly_get_match_counts - INFO - Argument --taxon_list_config: /Users/rprobst/Desktop/uce-analysis/datasets.conf 2020-05-01 07:19:13,011 - phyluce_assembly_get_match_counts - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/Users/rprobst/anaconda2/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 351, in main() File "/Users/rprobst/anaconda2/envs/phyluce/bin/phyluce_assembly_get_match_counts", line 329, in main len(organisms), TypeError: object of type 'NoneType' has no len()

probstrodolfo commented 4 years ago

Problem solved. Apparently I wasn't able to use 'datasets.conf' as a file name. Replacing it by 'samples.conf' worked.