Getting warning during tblastn

Question

[seta]

Dear all,

I'm trying to do tblastn (ncbi-blast2-2-30+ version) using fasta sequences of protein as a query and my de novo assembled transcriptome as a nucleotide database as following:

./tblastn -query arapr.fasta -db database1 -out tblastn1.txt -evalue 1e-3 -max_target_seqs 1 -num_threads 5 -outfmt 6

but the tblastn was completed with the following warning:

Warning: lcl|Query_18905 AT1G56045.1 pacid=19656851 transcript=AT1G56045.1 locus=AT1G56045 ID=AT1G56045.1.TAIR10 annot-version=TAIR10:
Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation.
Please verify the query sequence(s) and/or filtering options

Could anybody please help me to resolve the warning. Please don't refer me to the similar thread on biostar, I see it, but not useful for me.

Thanks for your help in advance.

Answer 1

[Sukhi Singh]

Check the nucleotide sequence that follows, if there is a bad character in it. There is a problem with this specific query.

Get the line number using

grep -n "Query_18905 AT1G56045.1" arapr.fasta

Remove the line to see if blast succeeds, e.g. if 10th line

sed 10d arapr.fasta | ./tblastn -i -db database1 -out tblastn1.txt -evalue 1e-3 -max_target_seqs 1 -num_threads 5 -outfmt 6