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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 - 'NoneType' object has no attribute 'groups' error #256

Open hutumpyancha opened 2 years ago

hutumpyancha commented 2 years ago

Dear Dr. Faircloth,

I am getting the mentioned error everytime I am trying to match the probes to my contigs. I saw that similar issues had been previously discussed on this page and on one such occassion, you had suggested making changes to the phyluce.config file. However, I am not sure I am understanding clearly what changes I should make and why. If you could assist me again with this error, it would be really helpful. The details are as follows -

(phyluce-1.7.1) [upasanag@qb2 upasanag]$ phyluce_assembly_match_contigs_to_probes --contigs /work/upasanag/spades-assemblies/contigs --probes /work/upasanag/190611-70B-OctoV2-Quattrini-baits.fas --output uce-search-results 2021-10-28 17:19:30,606 - phyluce_assembly_match_contigs_to_probes - INFO - ======= Starting phyluce_assembly_match_contigs_to_probes ======= 2021-10-28 17:19:30,607 - phyluce_assembly_match_contigs_to_probes - INFO - Version: 1.7.1 2021-10-28 17:19:30,607 - phyluce_assembly_match_contigs_to_probes - INFO - Commit: None 2021-10-28 17:19:30,607 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --contigs: /work/upasanag/spades-assemblies/contigs 2021-10-28 17:19:30,608 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --csv: None 2021-10-28 17:19:30,608 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --dupefile: None 2021-10-28 17:19:30,608 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --keep_duplicates: None 2021-10-28 17:19:30,608 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --log_path: None 2021-10-28 17:19:30,608 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_coverage: 80 2021-10-28 17:19:30,609 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --min_identity: 80 2021-10-28 17:19:30,609 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --output: /ddnA/qb2work/upasanag/uce-search-results 2021-10-28 17:19:30,609 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --probes: /work/upasanag/190611-70B-OctoV2-Quattrini-baits.fas 2021-10-28 17:19:30,609 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --regex: ^(uce-\d+)(?:_p\d+.*) 2021-10-28 17:19:30,610 - phyluce_assembly_match_contigs_to_probes - INFO - Argument --verbosity: INFO Traceback (most recent call last): File "/home/upasanag/.conda/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 421, in main() File "/home/upasanag/.conda/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 293, in main for seq in SeqIO.parse(open(args.probes, "rU"), "fasta") File "/home/upasanag/.conda/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 293, in for seq in SeqIO.parse(open(args.probes, "rU"), "fasta") File "/home/upasanag/.conda/envs/phyluce-1.7.1/bin/phyluce_assembly_match_contigs_to_probes", line 284, in new_get_probe_name return match.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups'

brantfaircloth commented 2 years ago

It looks like you are using a non-standard set of baits/probes (e.g. not one of those I provide). Specifically, that this is Andrea's bait set for octocorals, and I am not entirely sure what's in version 2. So, it would be easiest to contact her to see what she recommends for use as the bait-finding regular expression.

hutumpyancha commented 2 years ago

Thank you so much for your suggestion; I contacted her and now it seems to work with a different version of the probes fasta file.