blast retrieves "N/A" for taxonomic data
0
0
Entering edit mode
4 months ago
langziv • 0

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!

blast blastn • 170 views
ADD COMMENT
0
Entering edit mode

NCBI taxonomy is notoriously inaccurate and incomplete. Are you sure this data exists for this entry? Have you verified any other way?

ADD REPLY
0
Entering edit mode

Thank you for the reply. The "N/A" is in every line in the results. There's not a single line that contains taxonomic data other that the taxid. It's weird because the database in on the computer I work with, not an NCBI server, at the same path as the nucleotides database. I'm guessing it's some bug in the blast software.

I thought I could try to find a software that allows retrieving such data after providing the daxid.

ADD REPLY
0
Entering edit mode

Is it this line?: export BLASTDB="/.../biodb/BLAST/nucleotide3/taxdb"

That line/filepath looks malformed to me? Starts with /.../

ADD REPLY
0
Entering edit mode

That's not the whole line. I replaced part of it with "...".

ADD REPLY

Login before adding your answer.

Traffic: 1908 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6