The BLAST command stops with an error.
Entering edit mode
14 months ago
Riku ▴ 80

Hi all.

I would like to evaluate the assembly quality by running BLAST to the fasta file output by Trinity. I ran the command as follows, but this job was stopped with an error message.

$ ~/miniconda3/envs/py27/bin/blastx \
-query /home/nkarim/avenae/trinity_even_out_dir/Trinity.300.longest.fasta \
-db /home/nkarim/blast/db/nr \
-outfmt 6 \
-evalue 1e-3 \
-out /home/nkarim/blast/output/avenae.out

Error: NCBI C++ Exception:
    T0 "/opt/conda/conda-bld/blast_1626166529662/work/blast/c++/src/corelib/ncbiobj.cpp", line 980: Critical: (CCoreException::eNullPtr) ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
     Stack trace:
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/ ???:0 ncbi::CObject::ThrowNullPointerException() offset=0xB7 addr=0x7ffff635daa7
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/ ???:0 ncbi::blast::CBlastTracebackSearch::Run() offset=0x9C2 addr=0x7ffff7863ba2
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/ ???:0 ncbi::blast::CLocalBlast::Run() offset=0x1659 addr=0x7ffff780acb9
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 CBlastxApp::x_RunMTBySplitDB() offset=0xDEF addr=0x555555576e8f
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 CBlastxApp::Run() offset=0x49 addr=0x555555578689
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/ ???:0 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x17B addr=0x7ffff62a3d6b
      /lustre7/home/lustre5/nkarim/miniconda3/envs/py27/bin/../lib/ncbi-blast+/ ???: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=0x5FE addr=0x7ffff62a752e
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0 main offset=0x77 addr=0x55555556f6a7
      /lib64/ ???:0 __libc_start_main offset=0xF5 addr=0x7ffff5c513d5
      /home/nkarim/miniconda3/envs/py27/bin/blastx ???:0  offset=0x1BFE9 addr=0x55555556ffe9

I'm working on a Linux environment using miniconda. I found some people having similar errors, but they seemed to be having Windows specific errors. What could be wrong with my command?

Thank you very much for your help!

RNA-seq BLAST Trinity blastx • 1.8k views
Entering edit mode

How much memory did you assign to this job? Newest blast version are quite memory-hungry so it is not unlikely it just ran out of memory.

Can you check the memory (and mem-usage) of that job/process ?

Entering edit mode

I appreciate for your advices.

I'm using a supercomputer called "DDBJ", and I asigned 64GB memory. Would I be able to run this with more memory?

Entering edit mode

yes, in default settings you will need much more mem assigned to that job, try with something like 200Gb and see what that gives

Entering edit mode

To find out how much memory you have:

cat /proc/meminfo | head

And then get the blastx version:

blastx -version

And check if your blastdb is ok:

blastdbcmd -info /home/nkarim/blast/db/nr

After that, you could try to install an older blast version. Try e.g. 2.9.0 or 2.10.1 Maybe they need a little less memory.

Entering edit mode

I appreciated your kind help.

I have ran the command according to you.

$ cat /proc/meminfo | head
MemTotal:       48941764 kB
MemFree:         7765348 kB
MemAvailable:   31985704 kB
Buffers:              24 kB
Cached:         24736940 kB
SwapCached:       703004 kB
Active:          6513052 kB
Inactive:       23077048 kB
Active(anon):    2328112 kB
Inactive(anon):  2655972 kB

Although I got this information, this is the information of login node. I was using another node in this job, and I asigned 64GB memory.

$ blastx -version
blastx: 2.12.0+
 Package: blast 2.12.0, build Jul 13 2021 09:03:00

It seemed I have latest version BLAST. I may need to downgrade BLAST with Anaconda.

$ blastdbcmd -info nr
  blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type]
    [-entry sequence_identifier] [-entry_batch input_file] [-ipg IPG]
    [-ipg_batch input_file] [-taxids taxonomy_ids] [-taxidlist input_file]
    [-info] [-tax_info] [-range numbers] [-strand strand]
    [-mask_sequence_with mask_algo_id] [-out output_file] [-outfmt format]
    [-target_only] [-get_dups] [-line_length number] [-ctrl_a]
    [-show_blastdb_search_path] [-list directory] [-remove_redundant_dbs]
    [-recursive] [-list_outfmt format] [-exact_length] [-long_seqids]
    [-logfile File_Name] [-version]

   BLAST database client, version 2.12.0+

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

Error: Too many positional arguments (1), the offending value: nr
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: nr

I also used the command you specified, but same error message was outputed. I thought there were too many paths, so I tried this command but an error occurred. In this case, which do you think the cause is BLAST version or database?

Entering edit mode

Sorry, try

  blastdbcmd -info -db /home/nkarim/blast/db/nr

If that works, then try a downgrade to 2.11. That is working fine for me.

Entering edit mode

Thank you for your many replies.

It doesn't seem to be working, so it seem that there is the problem in database.

$ blastdbcmd -info -db /home/nkarim/blast/db/nr
BLAST Database error: No alias or index file found for nucleotide database [/home/nkarim/blast/db/nr] in search path [/lustre7/home/lustre5/nkarim/blast::]

I downloaded as follows. Is there are problem? There are the files from "nr.00.tar.gz" to "nr.55.tar.gz" and their decompression files in the downloaded directory.

$ email="my email address" ncbi-blast-dbs nr
Entering edit mode

I have never used that download script, however make sure the files exist and are where you think they are:

ls -l /home/nkarim/blast/db/nr*

If that shows files, possibly your download is broken anyway, try using for db updates, it might be slower than the other script but is more reliable. Also:

    cd $HOME/blast/db/
    nohup --decompress nr &

and wait.... check nohup.out from time to time. Once you got 56 volume files you can try again.

Entering edit mode

Your command have worked. Just as you said, the files might be broken.

But I just asigned 600GB memory, and it seem the task is working. If this job goes to the end without a problem, then the problem might had been in the memory.

If an errors occured in this job, I will try to download again according to you. If I still get an error, I hope you can help me again.

Finally, thank you very much for your kind advices everytime!


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