AttributeError: 'NoneType' object has no attribute 'groups'

[Genomics-Bhuwan]

Note: It matched the contigs for all the samples except "Callosciurus_prevostii_FMNH235489" I am running given command and I would get the error as given below.

match contigs to probes

phyluce_assembly_match_contigs_to_probes \ --contigs /shared/jezkovt_bistbs_shared/Data/uce-tutorial/Contigs \ --probes uce-5k-probes.fasta \ --output /shared/jezkovt_bistbs_shared/Data/uce-tutorial/uce-search-results

2024-09-24 19:14:45,424 - phyluce_assembly_match_contigs_to_probes - INFO - Callosciurus_finlaysonii_trotteri_USNM221585: 28 (0.30%) uniques of 9325 contigs, 0 dupe probe matches, 2 UCE loci removed for matching multiple contigs, 1 contigs removed for matching multiple UCE loci 2024-09-24 19:15:03,019 - phyluce_assembly_match_contigs_to_probes - INFO - Callosciurus_finlaysonii_williamsoni_USNM240512: 4075 (7.78%) uniques of 52388 contigs, 0 dupe probe matches, 212 UCE loci removed for matching multiple contigs, 25 contigs removed for matching multiple UCE loci 2024-09-24 19:15:26,194 - phyluce_assembly_match_contigs_to_probes - INFO - Callosciurus_prevostii_FMNH235489: 4040 (6.22%) uniques of 64983 contigs, 0 dupe probe matches, 167 UCE loci removed for matching multiple contigs, 58 contigs removed for matching multiple UCE loci Traceback (most recent call last): File "/home/bistbs/miniconda2/envs/phyluce-1.7.3/bin/phyluce_assembly_match_contigs_to_probes", line 421, in main() File "/home/bistbs/miniconda2/envs/phyluce-1.7.3/bin/phyluce_assembly_match_contigs_to_probes", line 354, in main contig_name = get_contig_name(lz.name1) File "/home/bistbs/miniconda2/envs/phyluce-1.7.3/bin/phyluce_assembly_match_contigs_to_probes", line 279, in get_contig_name return match.groups()[0] AttributeError: 'NoneType' object has no attribute 'groups' (phyluce-1.7.3) [bistbs@mualhpcp26 PRD /shared/jezkovt_bistbs_shared/Data/uce-tutorial/Contigs]$

[brantfaircloth]

Where did this file of contigs come from? Seems like they have different names than expected.

[Genomics-Bhuwan]

This file is an outgroup and took it from another study for my purpose.

[brantfaircloth]

That's very likely the cause of the error you are seeing. Phyluce expects a certain contig naming pattern, so contigs you include need to follow that pattern. Alternatively, you can edit the config file to match the pattern.