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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_assembly_match_contigs_to_probes gives error AttributeError: 'NoneType' object has no attribute 'groups' #171

Closed claudiavaga closed 4 years ago

claudiavaga commented 4 years ago

Hi everyone,

I am trying to use the command phyluce_assembly_match_contigs_to_probes but I am getting this error:

2019-10-02 16:22:35,792 - phyluce_assembly_match_contigs_to_probes - INFO - ======= Starting phyluce_assembly_match_contigs_to_probes ======= 2019-10-02 16:22:35,793 - phyluce_assembly_match_contigs_to_probes - INFO - Version: git fatal: not a git repository: '/home/claudiavaga/miniconda2/envs/phyluce/lib/python2.7/site-packages/.git' 2019-10-02 16:22:35,793 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /home/claudiavaga/capture/assemblies/IGS050 2019-10-02 16:22:35,794 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None 2019-10-02 16:22:35,795 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None 2019-10-02 16:22:35,795 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: None 2019-10-02 16:22:35,795 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 80 2019-10-02 16:22:35,796 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 80 2019-10-02 16:22:35,796 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /home/claudiavaga/capture/uce-search-results-IGS050 2019-10-02 16:22:35,797 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /home/claudiavaga/capture/baits_designed_filtered.fas 2019-10-02 16:22:35,797 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*) 2019-10-02 16:22:35,797 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/home/claudiavaga/miniconda2/envs/phyluce/bin/phyluce_assembly_match_contigs_to_probes", line 342, in main() File "/home/claudiavaga/miniconda2/envs/phyluce/bin/phyluce_assembly_match_contigs_to_probes", line 245, in main uces = set(new_get_probe_name(seq.id, regex) for seq in SeqIO.parse(open(args.probes, 'rU'), 'fasta')) File "/home/claudiavaga/miniconda2/envs/phyluce/bin/phyluce_assembly_match_contigs_to_probes", line 245, in uces = set(new_get_probe_name(seq.id, regex) for seq in SeqIO.parse(open(args.probes, 'rU'), 'fasta')) File "/home/claudiavaga/miniconda2/envs/phyluce/bin/phyluce_assembly_match_contigs_to_probes", line 234, in new_get_probe_name return match.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups' baits_designed.txt

I am attaching the probes set that I am trying to use since it seems like the problem are the probes. Someone know what is going on?

Thank you! Claudia

brantfaircloth commented 4 years ago

The baits you are using do not follow the naming scheme that is expected by phyluce. you can modify the naming scheme using the options for phyluce_assembly_match_contigs_to_probes or rename your baits to follow the expected naming scheme (e.g. see https://github.com/faircloth-lab/uce-probe-sets/blob/master/uce-5k-probe-set/uce-5k-probes.fasta).

claudiavaga commented 4 years ago

Thank you Brant for your fast answer! I will try that.