blastn error - NCBI C++ Exception

Question

[sunnykevin97]

CMD:

 /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn -query /home/sun/data/softwares/evaluation/TransDecoder-TransDecoder-v5.5.0/SRR3632057.trim_trinity.cdhit.fasta.transdecoder_dir/longest_or
    fs.cds  -db nucldb/nucleotideDB -out nucl_blastn_1align_1e-30_1.txt -num_alignments 1 -evalue 1e-30 -num_threads 10 > blastn_2.log

Total no. of fasta sequences - 149532, I tried to run with the less sequences, pops up the same error. I checked in the forum, their was similar issues posted in the forum wasn't so helpful, currently I'm using ncbi-blast-2.11.0+. Suggestions, please.

**Error: NCBI C++ Exception:**
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_400117_130.14.18.128_9008__PrepareRelease_Linux64-Centos_1601968763/c++/compilers/unix/../../src/corelib/ncbiobj.cpp", line 981: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_400117_130.14.18.128_9008__PrepareRelease_Linux64-Centos_1601968763/c++/compilers/unix/../../src/app/blast/blast_app_util.cpp", line 789: Critical: (CCoreException::eNullPtr) BLAST::ncbi::BlastFormatter_PreFetchSequenceData() - Error pre-fetching sequence data 
     Stack trace:
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::CObject::ThrowNullPointerException() offset=0x2D5 addr=0x1c667d5
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::objects::CBioseq_Handle::x_GetInfo() const offset=0x1A addr=0x159167a
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::objects::CBioseq_Handle::IsSetInst_Length() const offset=0x6 addr=0x15937b6
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::objects::CBioseq_Handle::GetBioseqLength() const offset=0xB addr=0x159371b
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???: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=0x3AC addr=0xed386c
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::BlastFormatter_PreFetchSequenceData(ncbi::blast::CSearchResultSet const&, ncbi::CRef<ncbi::objects::CScope, ncbi::CObjectCounterLocker>, ncbi::blast::CFormattingArgs::EOutputFormat) offset=0x7F addr=0xa5522f
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 CBlastnApp::Run() offset=0xFD0 addr=0xa4ba70
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x833 addr=0x1b184a3
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???: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=0x93B addr=0x1b16f6b
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 main offset=0x88 addr=0xa4a938
      /usr/lib64/libc.so.6 ???:0 __libc_start_main offset=0xF5 addr=0x7f43b96da505
      /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn ???:0 /home/sun/data/softwares/ncbi/ncbi-blast-2.11.0+/bin/blastn() [0xa4a7f5] offset=0x0 addr=0xa4a7f5

[GenoMax]

Are there any blank fasta records containing no sequence in your data? Do you get the error right away or does the process run for some time and produces some results. If it does then you could look around the last record producing a result in your query file.

You are using both query and database that are nucleotide sequences correct?

[sunnykevin97]

I don't have any blank fasta records. The CDS sequences, generated using Transdecoder pipeline. I get the error right away, but I'm able to run blastp.

Yes, Nucleotide sequences of all organisms which is non-redundant, downloaded from ncbi ftp site. I build a database using non-redundant sequences using makeblastdb.

Suggestions please!

[lieven.sterck]

what was the cmdline you used to create the blastDB?

[sunnykevin97]

makeblastdb -in nt.fasta -title nucleotideDB -dbtype nucl -out nucleotideDB -parse_seqids > nucl.log

[lieven.sterck]

how do the sequence ID look like? are they very long? weird chars in them?

could also perhaps try to format the DB without the -parse_seqid parameter?

[sunnykevin97]

Worked.

[lieven.sterck]

what worked? the formatting or running the blast?

[sunnykevin97]

Running the blast, with out blastn error - NCBI C++ Exception.

[lieven.sterck]

ok, so now it all works?

if so then likely some sequence IDs are a bit funky causing the parsing of them to go off.

[lieven.sterck]

owkee, and what about the format of that longest_orfs.cds file?

[sunnykevin97]

Fasta.

[1030528762]

I have the same problem, could you tell me how to solve it？thank you very much!

[lieven.sterck]

not 100% sure but I assume it was 'solved' by formatting the blastDB without the -parse_seqid option .

[auriane.lacroix]

Hi ! Same problem but I use the command :

makeblastdb -in  /env/products/abricate/1.0.1/db/argannot/sequences -dbtype nucl

and I get :

Error: NCBI C++ Exception:
    T0 "/tmp/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/build_db.cpp", line 1053: Error: (CMultisourceException::eInvalid) BLASTDB::ncbi::CBuildDatabase::CreateDirectories() - You do not have write permissions on 'argannot'

Any idea ?

[lieven.sterck]

yes, it seems you don't have write permission on that argannot folder.

Either change the permissions for that location such that you can write there or use the -out parameter and tell the blast cmd where to put the formatted DB (where you do have write permission obviously)