Answers.Body: <p>Based on other <a href="https://www.biostars.org/p/9462173/" rel="nofollow noreferrer">posts elsewhere</a> it seems likely that there is something funky about your database. How did you generate it?</p>
  <p>Could you try to re-generate the db without the <code>-parse-seqids</code> flag?</p>
  
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Answers.Text: I agree, I think this is the error output *Attempt to access NULL pointer.* is a bad error and suggests there's a database problem. This doesn't appear to be a memory allocation issue. 14GB is big, but there's nothing in the error message to raise concern about that
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Body: <p>I am trying to run BLASTN on a 14GB Pseudomonas database using the command: blastn -db ~/pseudomonas-db/pseudomonas -query ~/desktop/inputfiles/poz176.fasta -out poz176-out -num_threads 8</p>
  <p>I get the following error:</p>
  <pre><code>Error: NCBI C++ Exception:
      T0 &quot;c++/include/corelib/ncbidiag.hpp&quot;, line 980: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
      T0 &quot;c++/include/corelib/ncbidiag.hpp&quot;, line 789: Critical: (CCoreException::eNullPtr) ncbi::BlastFormatter_PreFetchSequenceData() - Error pre-fetching sequence data 
       Stack trace:
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xA6 addr=0x7fa1ea902f76
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0  offset=0x209609 addr=0x7fa1eb653609
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0 ncbi::objects::CBioseq_Handle::IsSetInst_Length() const offset=0x9 addr=0x7fa1eb653a09
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0 ncbi::objects::CBioseq_Handle::GetBioseqLength() const offset=0xE addr=0x7fa1eb653dce
        /usr/lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::LoadSequencesToScope(std::vector&lt;ncbi::objects::CSeq_id_Handle, std::allocator&lt;ncbi::objects::CSeq_id_Handle&gt; &gt;&amp;, std::vector&lt;ncbi::CRange&lt;unsigned int&gt;, std::allocator&lt;ncbi::CRange&lt;unsigned int&gt; &gt; &gt;&amp;, ncbi::CRef&lt;ncbi::objects::CScope, ncbi::CObjectCounterLocker&gt;&amp;) offset=0x329 addr=0x7fa1ebd90e79
        blastn ???:0 ncbi::BlastFormatter_PreFetchSequenceData(ncbi::blast::CSearchResultSet const&amp;, ncbi::CRef&lt;ncbi::objects::CScope, ncbi::CObjectCounterLocker&gt;, ncbi::blast::CFormattingArgs::EOutputFormat) offset=0x5FE addr=0x555af7fb31ee
        blastn ???:0 CBlastnApp::Run() offset=0xFDC addr=0x555af7fa99ac
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x193 addr=0x7fa1ea84edd3
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string&lt;char, std::char_traits&lt;char&gt;, std::allocator&lt;char&gt; &gt; const&amp;) offset=0x61D addr=0x7fa1ea85032d
        blastn ???:0 main offset=0x6B addr=0x555af7fa7e5b
        /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xEA addr=0x7fa1ea38ed0a
        blastn ???:0 _start offset=0x2A addr=0x555af7fa876a
  </code></pre>
  <p>I tried changing memory allocation but that didn't seem to do anything. I'm not sure what this error is telling me. How do I get around this?</p>
  <p>(Had posted this on stackoverflow and was asked to post here)</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-02-02T15:59:05.350Z
Comments.Text: Your blast run command looks fine. I'd look at the answer below. You could try running it on a bigger machine (more CPU), but I think you'll get the same answer.
Comments.UserDisplayName: M__
Tags: <blast><ncbi>
Title: What does this BLASTN mean: Error pre-fetching sequence data?
ThreadText: # What does this BLASTN mean: Error pre-fetching sequence data?
  
  (Asked by: username_0 on 2024-02-02)
  
  I am trying to run BLASTN on a 14GB Pseudomonas database using the command: blastn -db ~/pseudomonas-db/pseudomonas -query ~/desktop/inputfiles/poz176.fasta -out poz176-out -num\_threads 8
  
  I get the following error:
  
  ```
  Error: NCBI C++ Exception:
      T0 "c++/include/corelib/ncbidiag.hpp", line 980: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
      T0 "c++/include/corelib/ncbidiag.hpp", line 789: Critical: (CCoreException::eNullPtr) ncbi::BlastFormatter_PreFetchSequenceData() - Error pre-fetching sequence data 
       Stack trace:
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xA6 addr=0x7fa1ea902f76
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0  offset=0x209609 addr=0x7fa1eb653609
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0 ncbi::objects::CBioseq_Handle::IsSetInst_Length() const offset=0x9 addr=0x7fa1eb653a09
        /usr/lib/ncbi-blast+/libxobjmgr.so ???:0 ncbi::objects::CBioseq_Handle::GetBioseqLength() const offset=0xE addr=0x7fa1eb653dce
        /usr/lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::LoadSequencesToScope(std::vector<ncbi::objects::CSeq_id_Handle, std::allocator<ncbi::objects::CSeq_id_Handle> >&, std::vector<ncbi::CRange<unsigned int>, std::allocator<ncbi::CRange<unsigned int> > >&, ncbi::CRef<ncbi::objects::CScope, ncbi::CObjectCounterLocker>&) offset=0x329 addr=0x7fa1ebd90e79
        blastn ???:0 ncbi::BlastFormatter_PreFetchSequenceData(ncbi::blast::CSearchResultSet const&, ncbi::CRef<ncbi::objects::CScope, ncbi::CObjectCounterLocker>, ncbi::blast::CFormattingArgs::EOutputFormat) offset=0x5FE addr=0x555af7fb31ee
        blastn ???:0 CBlastnApp::Run() offset=0xFDC addr=0x555af7fa99ac
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x193 addr=0x7fa1ea84edd3
        /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) offset=0x61D addr=0x7fa1ea85032d
        blastn ???:0 main offset=0x6B addr=0x555af7fa7e5b
        /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xEA addr=0x7fa1ea38ed0a
        blastn ???:0 _start offset=0x2A addr=0x555af7fa876a
  
  ```
  
  I tried changing memory allocation but that didn't seem to do anything. I'm not sure what this error is telling me. How do I get around this?
  
  (Had posted this on stackoverflow and was asked to post here)
  
  **Tags:** blast, ncbi
  
  > **Comments:**
  > **username_1**: Your blast run command looks fine. I'd look at the answer below. You could try running it on a bigger machine (more CPU), but I think you'll get the same answer.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-02-02. Score: 1
  
  Based on other [posts elsewhere](https://www.biostars.org/p/9462173/) it seems likely that there is something funky about your database. How did you generate it?
  
  Could you try to re-generate the db without the `-parse-seqids` flag?
  
  > **Comments:**
  > **username_1**: I agree, I think this is the error output *Attempt to access NULL pointer.* is a bad error and suggests there's a database problem. This doesn't appear to be a memory allocation issue. 14GB is big, but there's nothing in the error message to raise concern about that  
  
  ---
  
  