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Joseph7e / Assign-Taxonomy-with-BLAST

Assign taxonomy with blast, can be used for qiime
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taxonomy_assignment_BLAST.py: error: the following arguments are required: tax_file #5

Closed amygresham48 closed 2 years ago

amygresham48 commented 2 years ago

Hello, thanks for this useful resource!

I am trying to run the taxonomy_assignment_BLAST.py in linux as follows:

_python3 taxonomy_assignment_BLAST.py --length_percentage 70 --hits_to_consider 20 --blast_file ncbi_nt --output_dir dada_seqs_ITS2.fa expanded_ncbitaxonomy.tsv

So the _dada_seqsITS2.fa file is my sequence_file and the _expanded_ncbitaxonomy.tsv is my tax_file.

I get this error: _the following arguments are required: taxfile

So it doesn't appear to be recognising the .tsv? Have I formatted the code wrong somehow?

Many thanks,

Amy

amygresham48 commented 2 years ago

Figured it out! it was trying to use the .fa file as the --output_dir so specifying a name for the directory _Assignedtaxonomy fixed the error