bioinformaticsblastncbi

Local BLAST NCBI C++ Exception


I'm getting an error trying to to use blast v2.12 against a local nt database. I've downloaded nt twice from the ftp server thinking the first time it was corrupt but that didn't change anything.

My command is:

blastn -db nt -num_threads 8 -outfmt "6 qseqid sacc stitle ssciname nident qlen" -num_alignments 10000 -query QUERY > OUT.csv

The error is:

Error: NCBI C++ Exception:
    T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/objistrasnb.cpp", line 499: Error: byte 90: overflow error ( at [].[].gi)
    T0 "/build/ncbi-blast+-S1iyIZ/ncbi-blast+-2.9.0/c++/src/serial/member.cpp", line 769: Error: ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)

I've tried multiple queries. The following actually works:

TGTTCACACCTCACTTCTTAACTATTATATCATTATTTTGACAAACAGACTACAAATGTAATATTATTGGATTACATTTGTAGTACAAAAGGAGGAAGAGATGAAAAAAATTTATATTAGTGTGCTAGTTCTTTTACTAATTATGATTATAATAACTTGGTTATTCAAAGATGACGATATTGAGAAAACAATTAGTTCTATTGAAAAAGGAAACTATAACGAAGTATATAAAAATAGTTCAGAAAAATCTAAACTGGCATATGGAGAAGAAGAAATTGTAGATAGGAATAAAAAAATTTACAAAGATTTAAGTGTCAATAACTTAAAAATTACTAATCATGAAATTAAAAAAACTGGAAAAGATAAAAAGCAAGTTGATGTTAAATATAACATATATACAAAATATGGAACTATACGACGTAATACACAATTAAACTTTATTTATGAAGATAAGCATTGGAAATTAGATTGGAGACCAGACGTAATAGTACCTGGTTTGAAAAATGGACAGAAAATTAATATAGAAACATTAAAATCAGAGCGAGGCAAAATAAAAGATAGAAATGGTATAGAATTAGCTAAAACTGGAAATACATATGAAATCGGTATTGTCCCTAACAAAACACCCAAAGAAAAATATGATGATATTGCTCGTGACTTACAAATTGATACAAAAGCTATAACCAATAAAGTTAATCAAAAATGGGTTCAGCCAGATTCATTTGTACCAATTAAAAAGATAAATAAACAAGATGAATATATAGACAAATTAATTAAATCATACAATTTACAAATAAACACTATAAAAAGCCGTGTTTATCCATTGAACGAAGCAACAGTACACCTTTTAGGTTATGTGGGTCCAATTAATTCTGACGAGTTAAAAAGTAAGCAATTTAGAAACTATAGCAAAAATACTGTTATTGGAAAAAAAGGCTTAGAACGCCTCTATGATAAACAATTGCAAAACACTGATGGTTTTAAGGTATCCATTGCAAATACTTATGACAATAAACCTTTAGACACATTATTGGAGAAAAAGGCTGAAAACGGAAAAGATCTTCATTTAACTATAGATGCTAGAGTACAAGAAAGTATTTATAAACATATGAAAAATGACGATGGATCTGGTACAGCATTACAACCAAAAACTGGAGAAATTTTAGCTTTGGTAAGTACCCCATCGTACGATGTTTATCCATTCATGAATGGATTAAGCAATAATGACTACCGTAAATTAACTAACAATAAAAAAGAGCCTTTGCTCAACAAATTTCAAATCACTACATCACCAGGTTCAACCCAAAAAATATTAACATCTATTATAGCCTTAAAAGAAAATAAACTAGACAAAAATACTAATTTTGATATTTATGGTAAGGGTTGGCAAAAAGATGCATCATGGGGTAATTATAATATCACAAGATTTAAAGTAGTAGACGGCAATATCGATTTAAAGCAAGCAATAGAATCATCAGACAACATATTTTTTGCCCGCATTGCATTAGCATTAGGAGCCAAAAAATTTGAGCAAGGTATGCAAGATTTGGGAATCGGTGAAAATATCCCGAGTGATTATCCCTTTTATAAAGCACAAATCTCAAATAGTAATTTAAAAAATGAAATATTATTAGCAGATTCAGGATATGGCCAAGGCGAGATACTAGTAAACCCTATACAAATTTTATCAATATACAGTGCTTTAGAAAATAACGGAAATATACAAAATCCTCATGTTTTACGTAAAACAAAATCTCAAATATGGAAAAAAGATATTATACCTAAAAAAGACATAGATATATTAACTAATGGTATGGAACGTGTAGTTAATAAAACACATAGGGATGATATATACAAAAATTATGCCCGAATTATTGGTAAATCTGGCACAGCAGAATTAAAAATGAATCAAGGGGAAACTGGAAGACAAATAGGTTGGTTTGTTTCATATAATAAAAATAATCCTAATATGTTAATGGCGATTAATGTTAAAGACGTTCAAAATAAAGGGATGGCCAGCTATAATGCTACTATATCTGGAAAAGTTTATGATGATTTGTATGATAATGGAAAAACTCAATTTGATATAGATCAGTAATTCGAATACTTCTTTTGACTTGGTATTAATTAAAAATAATAGTGAGAAGCGTTTCCACAAAGATTACATTTGTAATATATAGGAGGAATAAAATTGAAAA

But this one (and others) do not work:

ATGAAAAAGATAAAAATTGTTCCACTTATTTTAATAGTTGTAGTTGTCGGGTTTGGTATATATTTTTATGCTTCCAAAGATAAAGAAATTAATAATACTATTGATGCAATTGAAGATAAAAATTTCAAACAAGTTTATAAAGATAGCAGTTATATTTCTAAAAGCGATAATGGTGAAGTAGAAATGACTGAACGTCCGATAAAAATATATAATAGTTTAGGCGTTAAAGATATAAACATTCAGGATCGTAAAATAAAAAAAGTATCTAAAAATAAAAAACGAGTAGATGCTCAATATAAAATTAAAACAAACTACGGTAACATTGATCGCAACGTTCAATTTAATTTTGTTAAAGAAGATGGTATGTGGAAGTTAGATTGGGATCATAGCGTCATTATTCCAGGAATGCAGAAAGACCAAAGCATACATATTGAAAATTTAAAATCAGAACGTGGTAAAATTTTAGACCGAAACAATGTGGAATTGGCCAATACAGGAACAGCATATGAGATAGGCATCGTTCCAAAGAATGTATCTAAAAAAGATTATAAAGCAATCGCTAAAGAACTAAGTATTTCTGAAGACTATATCAAACAACAAATGGATCAAAATTGGGTACAAGATGATACCTTCGTTCCACTTAAAACCGTTAAAAAAATGGATGAATATTTAAGTGATTTCGCAAAAAAATTTCATCTTACAACTAATGAAACAAAAAGTCGTAACTATCCTCTAGGAAAAGCGACTTCACATCTATTAGGTTATGTTGGTCCCATTAACTCTGAAGAATTAAAACAAAAAGAATATAAAGGCTATAAAGATGATGCAGTTATTGGTAAAAAGGGACTCGAAAAACTTTACGATAAAAAGCTCCAACATGAAGATGGCTATCGTGTCACAATCGTTGACGATAATAGCAATACAATCGCACATACATTAATAGAGAAAAAGAAAAAAGATGGCAAAGATATTCAACTAACTATTGATGCTAAAGTTCAAAAGAGTATTTATAACAACATGAAAAATGATTATGGCTCAGGTACTGCTATCCACCCTCAAACAGGTGAATTATTAGCACTTGTAAGCACACCTTCATATGACGTCTATCCATTTATGTATGGCATGAGTAACGAAGAATATAATAAATTAACCGAAGATAAAAAAGAACCTCTGCTCAACAAGTTCCAGATTACAACTTCACCAGGTTCAACTCAAAAAATATTAACAGCAATGATTGGGTTAAATAACAAAACATTAGACGATAAAACAAGTTATAAAATCGATGGTAAAGGTTGGCAAAAAGATAAATCTTGGGGTGGTTACAACGTTACAAGAAATAAAGTGGTAAATGGTAATATCGACTTAAAACAAGCAATAGAATCATCAGATAACATTTTCTTTGCTAGAGTAGCACTCGAATTAGGCAGTAAGAAATTTGAAAAAGGCATGAAAAAACTAGGTGTTGGTGAAGATATACCAAGTGATTATCCATTTTATAATGCTCAAATTTCAAACAAAAATTTAGATAATGAAATATTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTAACCCAGTACAGATCCTTTCAATCTATAGCGCATTAGAAAATAATGGCAATATTAACGCACCTCACTTATTAAAAGACACGAAAAACAAAGTTTGGAAGAAAAATATTATTTCCAAAGAAAATATCAATCTATTAACTGATGGTATGCAACAAGTCGTAAATAAAACACATAAAGAAGATATTTATAGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGCAGAACTCAAAATGAAACAAGGAGAAACTGGCAGACAAATTGGGTGGTTTATATCATATGATAAAGATAATCCAAACATGATGATGGCTATTAATGTTAAAGATGTACAAGATAAAGGAATGGCTAGCTACAATGCCAAAATCTCAGGTAAAGTGTATGATGAGCTATATGAGAACGGTAATAAAAAATACGATATAGATGAATAA

Depending on the query, the byte value in the second line of the error changes. It does seem like there's an issue with the database, but I have downloaded it twice and am getting the same error.


Solution

  • Simple solution, BLAST version was not current using sudo apt-get. Download latest blast executables from NCBI FTP and the issue should go away if it is the same