Problems running local Blastp: No hits found when there should be

Question

[weslfield]

Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results.

blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml -outfmt 5 -query /Users/Wes/Desktop/new_pairwise/gyra_ref.txt -db blastdb

Here is the XML output from blastp:

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastp</BlastOutput_program>
  <BlastOutput_version>BLASTP 2.2.28+</BlastOutput_version>
  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs"", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>blastdb</BlastOutput_db>
  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
  <BlastOutput_query-def>gi|85676699|dbj|BAE77949.1| 30S ribosomal subunit protein S12 [Escherichia coli str. K12 substr. W3110]</BlastOutput_query-def>
  <BlastOutput_query-len>124</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
  <Iteration_iter-num>1</Iteration_iter-num>
  <Iteration_query-ID>Query_1</Iteration_query-ID>
  <Iteration_query-def>gi|85676699|dbj|BAE77949.1| 30S ribosomal subunit protein S12 [Escherichia coli str. K12 substr. W3110]</Iteration_query-def>
  <Iteration_query-len>124</Iteration_query-len>
<Iteration_hits>
</Iteration_hits>
  <Iteration_stat>
    <Statistics>
      <Statistics_db-num>5631</Statistics_db-num>
      <Statistics_db-len>4798969</Statistics_db-len>
      <Statistics_hsp-len>82</Statistics_hsp-len>
      <Statistics_eff-space>182163534</Statistics_eff-space>
      <Statistics_kappa>0.041</Statistics_kappa>
      <Statistics_lambda>0.267</Statistics_lambda>
      <Statistics_entropy>0.14</Statistics_entropy>
    </Statistics>
  </Iteration_stat>
  <Iteration_message>No hits found</Iteration_message>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

[Ram]

Could you maybe confirm that blastdb is a protein DB, please? I know it is a silly thing, but let's make sure our premise is perfect.

[Istvan Albert]

Also you have .txt file as input query - it could be still a fasta file but calling it that would be wrong and if you name your files with non matching extensions you can get confused really fast