1
$\begingroup$

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)

$\endgroup$
1
  • 1
    $\begingroup$ 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. $\endgroup$
    – M__
    Commented Feb 2 at 15:59

1 Answer 1

1
$\begingroup$

Based on other posts elsewhere 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?

$\endgroup$
1
  • 1
    $\begingroup$ 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 $\endgroup$
    – M__
    Commented Feb 2 at 15:56

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.