Question: [Ncbi-Blast-2.2.28+] Thrownullpointerexception() When Running Blastn
gravatar for tchnl
5.4 years ago by
tchnl20 wrote:


I'm still rather new to blast+ and I'm trying to get an implemented tool to work locally(that already works somewhere else). The tool just completely skips blasting and doesn't even show me any error. It creates and fills all the required files perfectly, makes the database files and then tries to run the blastn module. But nothing happens. I just get a completely blank blast_output file. No errors in my error logs. So I tried to do some of the commands manually in the terminal.

Here is the makeblastdb command:

/home/student1/MGCV_liteTools/ncbi-blast-2.2.28+/bin/makeblastdb -in /var/www/localhost/blast_tmp/1386165610refseq_upload_file.fasta
-input_type fasta -max_file_sz 3500000000 -dbtype nucl -out /var/www/localhost/blast_tmp/1386165610_db

It seems to work fine, as I get the following result:

Building a new DB, current time: 12/04/2013 15:01:54
New DB name:   /var/www/localhost/blast_tmp/1386165610_db
New DB title:  /var/www/localhost/blast_tmp/1386165610refseq_upload_file.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 3500000000B
Adding sequences from FASTA; added 7 sequences in 0.137179 seconds.

Then, I try to enter the blastn command:

/home/student1/MGCV_liteTools/ncbi-blast-2.2.28+/bin/blastn -db /var/www/localhost/blast_tmp/1386165610_db -query /var/www/localhost/blast_tmp/1386165610query_upload_file.fasta -evalue 0.001 -num_threads 4 -max_target_seqs 2000 -out /var/www/localhost/blast_tmp/1386165610blast.out -outfmt 5

The following error shows up:

Error: NCBI C++ Exception:
    "/home/student1/MGCV_liteTools/ncbi-blast-2.2.28+-src/c++/src/corelib/ncbiobj.cpp", line 925: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

Now I find it weird that I still get this error from the source map, even though I've deleted it already, and only kept the compiled version.

As I'm still very new to this, I tried some things to the best of my possibilities:

  • validating the fasta's: both were correct;
  • reinstall blast+: tried both the x32.tar.gz and the source one(and compiled it), still same error;
  • tried changing num_threads to 1 and 2: didn't work.

Is anyone able to see what I'm doing wrong here?


It still doesn't work, but atleast the tool is able to catch the error. Still no idea why it appears though.

ncbi ubuntu blast+ error linux • 5.5k views
ADD COMMENTlink modified 5.4 years ago by 5heikki8.4k • written 5.4 years ago by tchnl20

Looks like you might have found a bug. I suggest you contact the NCBI BLAST folks via

ADD REPLYlink written 5.4 years ago by Hamish3.1k
gravatar for 5heikki
5.4 years ago by
5heikki8.4k wrote:

You tried to make it from source? Why not just get a binary? Anyway, the answer is that you almost certainly compiled it wrong somehow. This file should work with ubuntu. Alternatively you could probably just apt-get install blast. The ia32 binaries are for itanium architecture..

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by 5heikki8.4k

The 'ia32' binaries are for 32-bit x86 systems. The Itanium binaries were tagged as 'ia64', and were discontinued after legacy NCBI BLAST 2.2.22. As far as I can see Itanium NCBI BLAST+ binaries have not been distributed by NCBI. The 'x64' binaries are for x86_64 (aka. 64-bit x86) systems.

On Linux and OS X systems (and any other UNIX style system) you can get the details of the current architecture using 'uname', for example on a Ubuntu 12.04 LTS for x86_64 system:

$ uname -a
Linux drosera-ubuntu1204 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Hamish3.1k

Thanks, it indeed was my clumsiness of having it compiled wrong. I used the 32bit version again and tested it, it now works (don't exactly know why it didn't the first time, but okay). As I said, I'm still new to this :).

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by tchnl20
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