error when running phyluce_assembly_match_contigs_to_probes

[fanvanf]

Hello! I have been trying to run phyluce_assembly_match_contigs_to_probes and after testing some different probe name formats I still can't make it to run... I get this error ； ‘====== Starting phyluce_assembly_match_contigs_to_probes ======= 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Version: git fatal: git fatal: Not a git repository: '/home/train/anaconda3/envs/fcx2.7/lib/python2.7/site-packages/.git' 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /root/contigs 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: None 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 80 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 80 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /root/uce-search-results 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /root/Target_Locus_Set.fasta 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*) 2019-06-14 19:49:19,460 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/root/CTD/miniconda/envs/phyluce/bin/phyluce_assembly_match_contigs_to_probes", line 342, in main() File "/root/CTD/miniconda/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 "/root/CTD/miniconda/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 "/root/CTD/miniconda/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'‘’` Here is the code： phyluce_assembly_match_contigs_to_probes \ --contigs contigs \ --probes Target_Locus_Set.fasta \ --output uce-search-results And I can't also run phyluce_assembly_assemblo_trinity.py .It is the same error : git fatal: Not a git repository: '/home/train/anaconda3/envs/fcx2.7/lib/python2.7/site-packages/.git' I reinstall the phyluce，and the problem is still . So what should I do to slove this iproblem?

[brantfaircloth]

Are you using baits that you designed? If you’re using the “official” UCE baits, you should not need to change anything.

[fanvanf]

Are you using baits that you designed? If you’re using the “official” UCE baits, you should not need to change anything. It works when using the "official"UCE baits.Tks

[brantfaircloth]

ok. if you send an example of the header of your bait file, I may be able to suggest a regular expression that will work.

[zivlie]

Hi Dr. Faircloth, I'm having a similar issue matching contigs to non-standard baits with the same error messages. In my case I'm using published mt genomes. The headers in the fasta file (converted from .gb) are either in the format ">TPA_INF: PSEUDOMYRMEX GRACILIS MITOCHONDRION, COMPLETE GENOME." or ">TPA: PSEUDOMYRMEX JANZENI MITOCHONDRION, COMPLETE GENOME.". I've had no issues matching the contigs to the official baits so I don't think its a simple issue with pathnames etc. The code I'm using:

phyluce_assembly_match_contigs_to_probes \
--contigs <path to contigs> \
--probes <path to probes> \
--output <output> \
--regex='^>TPA.*GENOME\.'

I've also tried using capturing groups in the regexp and had the same results. When I filter the .fasta in my shell by grepping with the expression above it correctly returns each name.