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  • tblastx error-ncbi-blast-2.2.26+

    Hello all,
    I am using ncbi-blast-2.2.26+ version on Linux machine (64 bit) with Fedora 16 OS. I have tried tblastx with my local nucleotide database
    against ensembl fish cDNA sequence. I have followed these steps

    1.makeblastdb -in example.fa -dbtype nucl -out example_nucl -logfile example_nuclblast.log

    2.tblastx -db example_nucl -query fish.fa -out tblastx_result.tsv -max_target_seqs 20 -evalue 1e-10 -outfmt "7 qseqid sseqid pident length mismatch gaps qstart qend sstart send sqlen slen evalue bitscore" -num_threads 32

    I get error

    Error: NCBI C++ Exception:
    "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_1540_130.14.18.6_9051_1329940081/rpmbuild/BUILD/ncbi-blast-2.2.26+/c++/src/objtools/alnmgr/alnmap.cpp", line 733: Error: CAlnVec::x_GetSeqLeftSeg(): Invalid Dense-seg: Row 0 contains gaps only.


    Can you tell me why tblastx creating error. It outputs file but stops in between.

    I tried looking source file at line no 00733



    Any help is appreciated

  • #2
    It looks like a bug - please report this to the NCBI BLAST team via the email address on their webpage, blast-help (at) ncbi.nlm.nih.gov

    Comment


    • #3
      happens to me too, no idea why. they went to next ver and still it happens.

      Comment


      • #4
        Perhaps bioman1 didn't report the bug, in which case it is hardly surprising the NCBI haven't fixed it. Could you (also) report the bug - a simple reproducible example would be ideal.

        Comment


        • #5
          it will be complicated to give a simple example, since I got no idea where the problem in my query fasta file is. I will be able to report this bug only after my data can be made publicly available... I too am using Fedora, so it seems this is either a redhat bug, or fedora only.

          Comment


          • #6
            I am not sure, but how about using formatdb instead of makeblastdb?

            HTH

            Edit: formatdb is discontinuated but I have used it recently with apparently no errors when running blast 2.26+
            Last edited by dnusol; 01-17-2013, 03:34 AM.

            Comment


            • #7
              Hey, I've encountered this error if one of the input files is not readable (in my case I invoked the tblastx in a wrong directory and the relative paths to the files were wrong).

              Hope that helps.

              Comment


              • #8
                Hi pschwien, that information should be very useful to the NCBI BLAST+ team - please email them about this (since they don't have a public bug tracker).

                Comment

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