Question: blastp NCBI C++ exception error: ThrowNullPointerException()
gravatar for garfield320
6 months ago by
garfield3200 wrote:

I'm running BLAST locally on WSL2 on Windows using Ubuntu platform. I'm getting this error when I run this blast command:

blastp -query /mnt/c/Users/username/Desktop/SIT/SIT_query.txt -db /mnt/c/Users/username/Desktop/SIT/db/SITaa -out SIT.blast.txt -evalue 1e-10 -outfmt "6 qseqid sseqid evalue stitle" -max_target_seqs 1000

Error: NCBI C++ Exception:   
T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/corelib/ncbiobj.cpp", line 980: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.       
Stack trace: 
/usr/lib/ncbi-blast+/ ???:0 ncbi::CStackTraceImpl::CStackTraceImpl() offset=0x4E addr=0x7f738780bb9e
/usr/lib/ncbi-blast+/ ???:0 ncbi::CStackTrace::CStackTrace(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) offset=0x23 addr=0x7f738780bc63
/usr/lib/ncbi-blast+/ ???:0 ncbi::CException::x_GetStackTrace() offset=0x95 addr=0x7f738788e095
/usr/lib/ncbi-blast+/ ???:0 ncbi::CException::SetSeverity(ncbi::EDiagSev) offset=0x66 addr=0x7f738788edc6
/usr/lib/ncbi-blast+/ ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xB6 addr=0x7f73878c7a6
/usr/lib/ncbi-blast+/ ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x9C7 addr=0x7f7388c77cd7
/usr/lib/ncbi-blast+/ ???:0 ncbi::blast::CLocalBlast::Run() offset=0x2268 addr=0x7f7388c1cdf8
blastp ???:0 CBlastpApp::Run() offset=0xDE5 addr=0x5620e435e335
/usr/lib/ncbi-blast+/ ???:0 ncbi::CNcbiApplication::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x173 addr=0x7f7387814b33                           /usr/lib/ncbi-blast+/ ???:0 ncbi::CNcbiApplication::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=0x5BD addr=0x7f738781664d                                                                                         blastp ???:0 main offset=0x6F addr=0x5620e435c26f  
/lib/x86_64-linux-gnu/ ???:0 __libc_start_main offset=0xF3 addr=0x7f73873360b3
blastp ???:0 _start offset=0x2E addr=0x5620e435d3ae

I've looked up a few questions that report similar errors and saw that people were suggesting there's something wrong with either the fasta query file or compiling blast, but I'm really confused because I ran this exact same command using the same query and database just yesterday and it worked. I've uninstalled blast with sudo apt-get remove ncbi-blast+ and sudo apt-get purge ncbi-blast+ then reinstalled it using sudo apt-get install ncbi-blast+ and I still get the same error. Can people give me any other suggestions why I'm suddenly getting this error?

blast • 286 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by garfield3200

can you double check the memory usage of this blast run. I' ve seen this error pop up when it ran out of memory. the newest blast version can consume very large amount of memory.

ADD REPLYlink written 6 months ago by lieven.sterck9.4k

I couldn't figure out how to check the memory usage - I did learn that I have 10.5GB of free RAM on my desktop (with free -m command) though. But I think you're right in that it could be a memory issue, because I tried running the same query file against a smaller local database (~60MB) and the search went through successfully (vs. the larger database that I've been trying to use is ~2.5GB). I'm not sure how to solve this issue if it is indeed a memory problem. Should I try downgrading my current version of blast?

ADD REPLYlink written 5 months ago by garfield3200

downgrading might work indeed. or you run it on a more powerful machine? do you have access to an HPC or such? or compute server?

ADD REPLYlink written 5 months ago by lieven.sterck9.4k
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