The BLAST command stops with an error.

The BLAST command stops with an error.

0

Hi all.

I would like to evaluate the assembly quality by running BLAST to the fasta file output by Trinity.
I ran the command as follows, but this job was stopped with an error message.

$ ~/miniconda3/envs/py27/bin/blastx 
-query /home/nkarim/avenae/trinity_even_out_dir/Trinity.300.longest.fasta 
-db /home/nkarim/blast/db/nr 
-outfmt 6 
-evalue 1e-3 
-out /home/nkarim/blast/output/avenae.out

Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1626166529662/work/blast/c++/src/corelib/ncbiobj.cpp", line 980: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
     Stack trace:
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xB7 addr=0x7ffff635daa7
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x9C2 addr=0x7ffff7863ba2
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CLocalBlast::Run() offset=0x1659 addr=0x7ffff780acb9
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 CBlastxApp::x_RunMTBySplitDB() offset=0xDEF addr=0x555555576e8f
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 CBlastxApp::Run() offset=0x49 addr=0x555555578689
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x17B addr=0x7ffff62a3d6b
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../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=0x5FE addr=0x7ffff62a752e
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 main offset=0x77 addr=0x55555556f6a7
      /lib64/libc.so.6 ???:0 __libc_start_main offset=0xF5 addr=0x7ffff5c513d5
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0  offset=0x1BFE9 addr=0x55555556ffe9

I’m working on a Linux environment using miniconda.
I found some people having similar errors, but they seemed to be having Windows specific errors.
What could be wrong with my command?

Thank you very much for your help!


RNA-seq


BLAST


Trinity


blastx

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