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BLAST+ taxonomic problem

hey i wrote simple script that checks number of hommologs and organism in tax but i have problem with orgnism number... its often 0 where number of homologues are for example 1000

part of my code:

os.system('blastp -query %s -db /home/xyl/nr/nr -seg no -outfmt 7
-taxidlist /home/xyl/blast_tax/taxids/eukarya.ids -evalue 1e-3 -out /home/xyl/blast_tax/results/%s -max_target_seqs 20000 -num_threads 8' % (file, fileout3))
os.system('blastp -query %s -db /home/xyl/nr/nr -seg no -outfmt 18 -taxidlist /home/xyl/blast_tax/taxids/eukarya.ids -evalue 1e-3 -out /home/xyl/blast_tax/results/%s -max_target_seqs 20000 -num_threads 8' % (file, fileouttax3))

i use taxidlist for example: https://mega.nz/file/atdRXa6B#77ntvE3wObEnzGi6peLrUW5HnU611K74ufsgvSb3Eto

protein blast
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written by Xylanaser Xylanaser

Does nr refer to preformatted blast database downloaded from NCBI?

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written by GenoMax GenoMax

yes, i use newest blast and db

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written by Xylanaser Xylanaser

Have you downloaded taxdb files from NCBI and are they in the same folder as the nr db?

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written by GenoMax GenoMax

1 answer

GenoMax sorry for late answer

Now it is work fine

there are two options:

  • corrupted database (on server or download)

I download it again

Now it is work fine

cheers

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written by Xylanaser Xylanaser

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