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.
I assume your are actually using a fasta format input instead of bare sequences. I tried your sequence at NCBI and there was no problem getting results so that does not seems to be an issue. You should add an explicit -task blastn or -task megablast to your command line and try. I also did a blastn (v. 2.12.0) against a local copy of nt and was able to get results without any issues.
While you say you are using v.2.12 the error above is referring to v.2.9. Are you sure you are running the correct blast? There may be more than one on your system. It is possible that you are using old blast against new v.5 nt indexes which require latest blast+.
You are absolutely correct about the version difference. I recently used sudo apt install ncbi-blast+ and assumed that installed the latest version of blast, but that obviously wasn't the case. The database is version 5, which explains the incompatibility.
Thank you for pointing that out! Problem solved.
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