Question: Problems running local Blastp: No hits found when there should be
0
gravatar for weslfield
4.5 years ago by
weslfield90
European Union
weslfield90 wrote:

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. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, 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>
 
blastp blast alignment • 1.2k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.5 years ago by weslfield90

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.

ADD REPLYlink written 4.5 years ago by RamRS20k

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

ADD REPLYlink written 4.5 years ago by Istvan Albert ♦♦ 79k
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