Question: Getting warning during tblastn
0
gravatar for seta
2.4 years ago by
seta920
Sweden
seta920 wrote:

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.

 

ADD COMMENTlink modified 2.4 years ago by Sukhdeep Singh9.0k • written 2.4 years ago by seta920
0
gravatar for Sukhdeep Singh
2.4 years ago by
Sukhdeep Singh9.0k
Netherlands
Sukhdeep Singh9.0k wrote:

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 , eg 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
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Sukhdeep Singh9.0k
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