Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.

Question

[hophuquy0944]

When I run blastn (version 2.15) and nt database (latest version) was extracted. I used aspera to download database from ncbi

This is code I used to download database:

ascp -T -i /home/hp/local/aspera/etc/asperaweb_id_dsa.openssh [e-mail]:/blast/db/nt.{000..140}.tar.gz/ ./

and this is code I used to run blastb:

blastn \
  -num_threads 40 \
  -query test2.fasta \
  -db ../../../database/database_nt/nt \
  -outfmt "6 qseqid sseqid pident length qlen slen evalue bitscore mismatch gapopen qstart qend sstart send" \
  -out ./test_output/dedup_total.tsv

I got this error:

> blastn -num_threads 40 -query test.fasta 
> -db ../../../database/database_nt/nt -outfmt "6 qseqid sseqid pident length qlen slen evalue bitscore mismatch gapopen qstart qend sstart
> send"  -out ./test_output/dedup_total.tsv Error: NCBI C++ Exception:
>     T0 "/opt/conda/conda-bld/blast_1699638441282/work/blast/c++/src/corelib/ncbiobj.cpp",
> line 1010: Critical: (CCoreException::eNullPtr)
> ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL
> pointer.
>      Stack trace:
>       /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxncbi.so
> ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xAB
> addr=0x149498eb419b
>       /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxblast.so
> ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0xB1D
> addr=0x14949ab0766d
>       /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxblast.so
> ???:0 ncbi::blast::CLocalBlast::Run() offset=0x1E40
> addr=0x14949aab5a60
>       blastn ???:0 CBlastnApp::x_RunMTBySplitDB() offset=0x1733 addr=0x557e1560f743
>       blastn ???:0 CBlastnApp::Run() offset=0x489 addr=0x557e15611349
>       /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxncbi.so
> ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char
> const, int, bool*) offset=0x19B addr=0x149498dfd9bb
>       /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/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=0x544 addr=0x149498e00234
>       blastn ???:0 main offset=0x77 addr=0x557e156067b7
>       /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xF3 addr=0x149498a72083
>       blastn ???:0  offset=0x1C0F9 addr=0x557e156070f9

if you have any solution for this problem please let me know

[Ram]

I've removed unneccessary tags - meta and how-to don't apply to this post at all, and the forum tag is not in use anymore.

[hophuquy0944]

sorry for that, this is first time i use it.

[Pierre Lindenbaum]

see blastp Error: NCBI C++ Exception: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer

[hophuquy0944]

my blast is latest version 2.15. I don't know what you want me to see in this link.

[Pierre Lindenbaum]

it looks like the same error.

[hophuquy0944]

they don't have clear answer for this problem. I run all subset of this data to find out error subsets database but it seem not any error in subsets. I tried with blast version 2.9 -> 2.15. but all of this version still had a same error.

[GenoMax]

Did you remeber to unzip/untar the nt preformatted files that you downloaded?

[hophuquy0944]

the nt database was extracted, and this is latest version of nt database in ncbi and blastn with version 2.15. I used many query file.fasta to test not just 1 file.

[GenoMax]

What OS are you using? Are you able to run blastn --help and does it produce the in-line help?

I used many query file.fasta

And those were all nucleotide sequences?

[hophuquy0944]

I'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work

(/data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4) quyho@worker-01:/data/quyho/tools/mgs2amr_tool/test$ blastn -h USAGE blastn [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename] [-seqidlist filename] [-negative_gilist filename] [-negative_seqidlist filename] [-taxids taxids] [-negative_taxids taxids] [-taxidlist filename] [-negative_taxidlist filename] [-no_taxid_expansion] [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm] [-subject subject_input_file] [-subject_loc range] [-query input_file] [-out output_file] [-evalue evalue] [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty] [-perc_identity float_value] [-qcov_hsp_perc float_value] [-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_options] [-filtering_db filtering_database] [-window_masker_taxid window_masker_taxid] [-window_masker_db window_masker_db] [-soft_masking soft_masking] [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value] [-best_hit_score_edge float_value] [-subject_besthit] [-window_size int_value] [-off_diagonal_range int_value] [-use_index boolean] [-index_name string] [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format] [-show_gis] [-num_descriptions int_value] [-num_alignments int_value] [-line_length line_length] [-html] [-sorthits sort_hits] [-sorthsps sort_hsps] [-max_target_seqs num_sequences] [-num_threads int_value] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION Nucleotide-Nucleotide BLAST 2.15.0+

Use '-help' to print detailed descriptions of command line arguments

[GenoMax]

How much memory do you have available? For nt database you are going to need 30-40G minimum. You may simply be running out of memory.

[hophuquy0944]

thank sir, i will check it again

[hophuquy0944]

i have the same error, i used high performance computer, here is my code to set memory.

srun --nodes=1 --ntasks=1 --cpus-per-task=24 --mem=70G  --pty /bin/bash 

but when i tried to run blastn again. the same error appear

blastn -query test2.fasta -db ../../../database/database_nt/nt -out result_000.txt -num_threads 1 -max_target_seqs 5
Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1699638441282/work/blast/c++/src/corelib/ncbiobj.cpp", line 1010: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - 
Attempt to access NULL pointer.
     Stack trace:
      /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xAB addr=0x152658e3f19b
      /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0xB1D addr=0x15265aa9266d
      /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CLocalBlast::Run() offset=0x1E40 addr=0x15265aa40a60
      blastn ???:0 CBlastnApp::x_RunMTBySplitDB() offset=0x1733 addr=0x563c2e8ee743
      blastn ???:0 CBlastnApp::Run() offset=0x489 addr=0x563c2e8f0349
      /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x19B addr=0x152658d889bb
      /data/quyho/tools/mgs2amr_tool/mgs2amr/mgs2amr_env4/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=0x544 addr=0x152658d8b234
      blastn ???:0 main offset=0x77 addr=0x563c2e8e57b7
      /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xF3 addr=0x1526589fd083
      blastn ???:0  offset=0x1C0F9 addr=0x563c2e8e60f9

[GenoMax]

Can you create a small test database (makeblastdb) from your query file and try to run the search against the same file and see if that works?

If it does not work then there is some kind of incompatibility with the NCBI blast executable and the OS/libraries you are running this on. You may need to download blast+ source code and build the executable on your computer yourself.

If the small search works then the other possibility is your copy of nt may be corrupt. You may need to try downloading that again.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted.

NOTE

DO NOT use the double quote option, it's not meant for code formatting and mangles the content that it formats.

[hophuquy0944]

thank you