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5 months ago
hophuquy0944
•
0
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 anonftp@ftp.ncbi.nlm.nih.gov:/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
I've removed unneccessary tags -
meta
andhow-to
don't apply to this post at all, and theforum
tag is not in use anymore.sorry for that, this is first time i use it.
see blastp Error: NCBI C++ Exception: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer
my blast is latest version 2.15. I don't know what you want me to see in this link.
it looks like the same error.
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.
Did you remeber to unzip/untar the
nt
preformatted files that you downloaded?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.
What OS are you using? Are you able to run
blastn --help
and does it produce the in-line help?And those were all nucleotide sequences?
I'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work
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.thank sir, i will check it again
i have the same error, i used high performance computer, here is my code to set memory.
but when i tried to run blastn again. the same error appear
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.Please use the formatting bar (especially the
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
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thank you