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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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question about example 5 step 3 #12

Closed zckoo007 closed 4 years ago

zckoo007 commented 4 years ago

when I run this step, I get an error

phylophlan_get_reference -g c__Espilonproteobacteria \
    -n -1 \
    -o input_bins \
    --verbose 2>&1 | tee logs/phylophlan_get_reference.log
phylophlan_get_reference.py version 0.16 (9 April 2020)

Command line: ../../phylophlan_get_reference.py -g c__Espilonproteobacteria -n -1 -o input_bins --verbose

Arguments: {'get': 'c__Espilonproteobacteria', 'list_clades': False, 'database_update': False, 'output_file_extension': '.fna.gz', 'output': 'input_bins', 'how_many': None, 'genbank_mapping': 'assembly_summary_genbank.txt', 'verbose': True}
File "taxa2genomes.txt" present
File "taxa2genomes_cpa201901_up201901.txt.bz2" present
Output folder "input_bins" present
File "assembly_summary_genbank.txt" present
[e] no reference genomes found for "c__Espilonproteobacteria", please check the taxonomic label provided
zckoo007 commented 4 years ago

I solve it change cEspilonproteobacteria to cEpsilonproteobacteria

fasnicar commented 4 years ago

Thanks, I corrected the typo.