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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Error in the "phyluce_assembly_match_contigs_to_probes.job" step #323

Open LauraGonzalezMozo opened 7 months ago

LauraGonzalezMozo commented 7 months ago

Dear all, I have tried to get my AHE sequences through the phyluce pipeline but am stuck on the "phyluce_assembly_match_contigs_to_probes.job". The error message I receive says "nonetype object has no attribute groups". I also get the error ". How can I avoid this error?

brantfaircloth commented 7 months ago

This is most likely the result of the probe/bait file you are using. If this is not a probe file for UCE data (you mention these are AHE data), then the structure of the file you are using is probably not what is expected by phyluce. The format of the probe file fasta header is described, somewhat, in the "Hint" box found here:

https://phyluce.readthedocs.io/en/latest/daily-use/daily-use-3-uce-processing.html

Specifically, this is the Hint box under "match contigs to probes". The actual format of the probe file can be seen here:

https://github.com/faircloth-lab/uce-probe-sets/blob/master/uce-5k-probe-set/uce-5k-probes.fasta

There are two ways to work with this - you can find a reasonable regular expression to match however probes/baits are named for your AHE data and input that to phyluce_assembly_match_contigs_to_probes (--regex option) or you could rename the probes/baits in the file you are using to match what is expected by phyluce.