Blast - problem with xml output
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Entering edit mode
9.9 years ago
rotmus0 • 0

I encountered a weird problem when I used blast(i'm using blastall 2.2.26).

I have a fasta file with 8 sequences and I'm running blast on it to get the xml output, the problem is I get 1-8 iterations as expected but in addition I get one more empty iteration with iter-num 1 after iteration 8(meaning I have two 1 iteration, one is good the other only have iter-num and statistics).

I have tried to examine the behavior but I can't get absolute results, sometimes it happens and sometimes it don't(it usually happens occasionally on small sets of sequences like 8). I looked every where searching for an explanation with no success.

I run the command:

blastall -p blastn -g F -q -9999 -i test.fasta -d /bio/db/blast/miRNA_hair -e 0.01 -m 7 -v 1 -b 1 -o ~pmrotem/checks/split_and_merge_blast/check.xml

Here is input(test.fasta) content:

>1 <unknown description>
AAAAAAAGGATGGAGGAAGATCTACCAAGCAAA
>2 <unknown description>
AAAAAAGACACCCCCCCCACCACC
>3 <unknown description>
AAAAAAGGAAGGAACTGGGACACGGGA
>4 <unknown description>
AAAAACTTGGATCCTGGCCGGGCGC
>5 <unknown description>
AAAAAGATGAGTGGTGAAAATCTGATC
>6 <unknown description>
AAAAAGCTAACACTCACCTGAGTTTTAAAAAACTC
>7 <unknown description>
AAAAAGCTCGTAGTTGGATCTTGGGA
>8 <unknown description>
AAAAAGCTCGTAGTTGGATCTTGGGATCGAGCGGGCGGTC

And here is the output(check.xml) content:

 < ?xml version="1.0" encoding="UTF-8"?>
 < !DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
    <BlastOutput>
  <BlastOutput_program>blastn</BlastOutput_program>
  <BlastOutput_version>blastn 2.2.26 [Sep-21-2011]</BlastOutput_version>
  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~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>/bio/db/blast/miRNA_hair</BlastOutput_db>
  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
  <BlastOutput_query-def>1 <unknown description></BlastOutput_query-def>
  <BlastOutput_query-len>33</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_expect>0.01</Parameters_expect>
      <Parameters_sc-match>1</Parameters_sc-match>
      <Parameters_sc-mismatch>-9999</Parameters_sc-mismatch>
      <Parameters_gap-open>0</Parameters_gap-open>
      <Parameters_gap-extend>0</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_query-ID>lcl|1_0</Iteration_query-ID>
      <Iteration_query-def>1 <unknown description></Iteration_query-def>
      <Iteration_query-len>33</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>2</Iteration_iter-num>
      <Iteration_query-ID>lcl|2_0</Iteration_query-ID>
      <Iteration_query-def>2 <unknown description></Iteration_query-def>
      <Iteration_query-len>24</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>3</Iteration_iter-num>
      <Iteration_query-ID>lcl|3_0</Iteration_query-ID>
      <Iteration_query-def>3 <unknown description></Iteration_query-def>
      <Iteration_query-len>27</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>4</Iteration_iter-num>
      <Iteration_query-ID>lcl|4_0</Iteration_query-ID>
      <Iteration_query-def>4 <unknown description></Iteration_query-def>
      <Iteration_query-len>25</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>5</Iteration_iter-num>
      <Iteration_query-ID>lcl|5_0</Iteration_query-ID>
      <Iteration_query-def>5 <unknown description></Iteration_query-def>
      <Iteration_query-len>27</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>6</Iteration_iter-num>
      <Iteration_query-ID>lcl|6_0</Iteration_query-ID>
      <Iteration_query-def>6 <unknown description></Iteration_query-def>
      <Iteration_query-len>35</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>7</Iteration_iter-num>
      <Iteration_query-ID>lcl|7_0</Iteration_query-ID>
      <Iteration_query-def>7 <unknown description></Iteration_query-def>
      <Iteration_query-len>26</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>8</Iteration_iter-num>
      <Iteration_query-ID>lcl|8_0</Iteration_query-ID>
      <Iteration_query-def>8 <unknown description></Iteration_query-def>
      <Iteration_query-len>40</Iteration_query-len>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>16772</Statistics_db-num>
          <Statistics_db-len>1687748</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>0</Statistics_eff-space>
          <Statistics_kappa>0.75</Statistics_kappa>
          <Statistics_lambda>1.38629</Statistics_lambda>
          <Statistics_entropy>1.38629</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
    </Iteration>
  </BlastOutput_iterations>
</BlastOutput>

btw, I noticed that it happens when I have no hits.

any suggestions anyone?
xml blast • 2.8k views
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There is a rendering bug, the XML header is not printed correctly, have added two spaces there.

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9.9 years ago

Have you tried using the new blastn from the blast+ package? The classic blast is not anymore actively developed and is now called legacy blast. I don't really know if it will solve your problem but in my experience I've found some bugs in the legacy blast package that are not there anymore in the blast+ latest.

See the blast+ downloads page. I would heartily recommend upgrading, it is not difficult to transform your old blast command parameters to the new ones and you will get all the benefits of an up-to-date software package actively developed and debugged.
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