Error while running blastn

Question

[Nir]

Hi

I am trying to run blastn on my database. I have created a database with 10,000 DNA sequences.

I used this command:

$ makeblastdb -in Phibro_db.fasta -input_type fasta -dbtype nucl -parse_seqids -title "Phibro_db"

In order to test it I made a fasta file with 2 sequences (which are present in the database): query.fasta, then I ran this command:

$blastn -db Phibro_db.fasta -query query.fasta -out results.out

I got this error message and I don't know what it means.

Thank you very much for your help...

Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1537409789918/work/c++/src/corelib/ncbiobj.cpp", line 977: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
     Stack trace:
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x56 addr=0x7f1f08694766
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CStackTrace::CStackTrace(std::string const&) offset=0x1F addr=0x7f1f086947ff
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CException::x_GetStackTrace() offset=0x64 addr=0x7f1f0870de84
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CException::SetSeverity(ncbi::EDiagSev) offset=0x54 addr=0x7f1f0870ef34
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CObject::ThrowNullPointerException() offset=0x9F addr=0x7f1f08740fcf
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x9FF addr=0x7f1f0ad15faf
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxblast.so ???:0 ncbi::blast::CLocalBlast::Run() offset=0x124D addr=0x7f1f0acbdd8d
      blastn ???:0 CBlastnApp::Run() offset=0x1052 addr=0x412592
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x113 addr=0x7f1f0869e483
      /home/qiime2/miniconda/envs/qiime2-2019.1/bin/../lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CNcbiApplication::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::string const&) offset=0x48D addr=0x7f1f086a006d
      blastn ???:0 main offset=0x5C addr=0x4101dc
      /lib/x86_64-linux-gnu/libc.so.6 ???:0 __libc_start_main offset=0xF3 addr=0x7f1f08274083
      blastn ???:0 blastn() [0x411369] offset=0x0 addr=0x411369

[Ram]

Please put some effort into formatting your post. When posted without proper formatting, your content looks like a wall of text, and no one spends time reading walls of text. I've done it for you this time.

[Nir]

Hi Ram, Sorry for that..... How do I format the post the way you did? (the bold area) Nir

[Ram]

The toolbar is your friend - experiment with it. You can also learn markdown, which is a way of formatting using simple metacharacters. For example, *italics* will become italics, **bold** -> bold, `code` -> code, ~~strikethrough~~ -> strikethrough etc. Google "Markdown formatting" for more info.

The code blocks can be created either by adding 4 spaces before each line like below:

line 1  
line 2

or by adding three back-ticks(`) at the beginning and end of the code block. The toolbar makes this easier. Just select the code block and tap on the 101010 button.

[Pierre Lindenbaum]

looks like a duplicate of The BLAST command stops with an error.

[Ram]

Wouldn't call it a duplicate - just that this error was seen and addressed in an earlier post.

[Nir]

Hi Pierre, Thanks a lot for your help. I have looked at the added post and tested my memory definitions:

MemTotal: 24044996 kB

MemFree: 15352968 kB

MemAvailable: 20993948 kB

Buffers: 524532 kB

Cached: 5110184 kB

SwapCached: 0 kB

Active: 4944520 kB

Inactive: 3064588 kB

Active(anon): 2375400 kB

Inactive(anon): 60804 kB

Blast version is 2.7.1

I appreciate your suggestions. Tx Nir

[GenoMax]

How much memory does your machine have? What is the size of that database file (besides the fact that it has 10K sequences)?

Answer 1

[Nir]

Hi, Just wanted to update that I looked at this post,

> blastn error - NCBI C++ Exception

and found the problem. I had to use the command without "parse_seqid".

Now the command works.

Thanks a lot for your help.

Nir