Hi,
I tried to manually create a CRUX reference database but I ran into an error.
This is the command I use: python <path_to>/entrez_qiime.py -i <path_to>//_fasta_taxonomy/example.fasta -o <path_to>//_fasta_taxonomy/_taxonomy -n <path_to_ncbi_Taxo_dump_directory>/TAXO -r <path_to_ncbi_accession2taxonomy_directory>/accession2taxonomy/nucl_gb.accession2taxid -r superkingdom,phylum,class,order,family,genus,species
This is the error:
Traceback (most recent call last):
File "/Users/joycevelos/Desktop/entrez_qiime/entrez_qiime.py", line 24, in
from cogent.parse.ncbi_taxonomy import NcbiTaxonomyFromFiles
ImportError: No module named cogent.parse.ncbi_taxonomy
Upon unzipping the taxdump files, I found no NcbiTaxonomyFromFiles in that and also in the NCBI page itself. I am not sure what's the problem. Could you please help me?
Best regards,
Joyce
Hi,
I tried to manually create a CRUX reference database but I ran into an error.
This is the command I use: python <path_to>/entrez_qiime.py -i <path_to>//_fasta_taxonomy/example.fasta -o <path_to>//_fasta_taxonomy/_taxonomy -n <path_to_ncbi_Taxo_dump_directory>/TAXO -r <path_to_ncbi_accession2taxonomy_directory>/accession2taxonomy/nucl_gb.accession2taxid -r superkingdom,phylum,class,order,family,genus,species
This is the error:
Traceback (most recent call last):
File "/Users/joycevelos/Desktop/entrez_qiime/entrez_qiime.py", line 24, in
from cogent.parse.ncbi_taxonomy import NcbiTaxonomyFromFiles
ImportError: No module named cogent.parse.ncbi_taxonomy
Upon unzipping the taxdump files, I found no NcbiTaxonomyFromFiles in that and also in the NCBI page itself. I am not sure what's the problem. Could you please help me?
Best regards,
Joyce