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2 hours ago by

Hello.

I'm trying to get taxonomic data, such as scientific and common names, and keep getting "N/A" for each taxonomic parameter. I updated the taxdb. It's in the same directory as the nucleotides database. I also tried specifying the path, as suggested in previous posts on similar issues.

The script is

export BLASTDB="/.../biodb/BLAST/nucleotide3/taxdb"

module load blast/blast-2.10.0

cd /.../output/blast

for file in ./*.fa; do 
  output=${file#"./scaffold_"}
  output=${output%.fa}
  output=${output}_blast.txt  
  blastn -query $file 
  -db /bioseq/biodb/BLAST/nucleotide3/nt 
  -max_hsps 1 -max_target_seqs 1 -num_threads 20 
  -out $output 
  -outfmt "6 qseqid sseqid pident staxids sscinames scomnames qstart qend length sstart send slen evalue mismatch gapopen bitscore"
done

Here's as example of one line form an output file:

scaffold_11 gi|1530013355|ref|XM_010738424.3| 97.059 215358 N/A N/A 68936 68969 34 1372 1339 2896 0.11 1 0 58.4

As can be seen data is retrieved except for where the taxonomic data is expected.

Thanks!

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modified 2 hours ago

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2 hours ago
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langziv0



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