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  • no qcovs output from standalone blast

    I am having trouble getting query coverage output from local/standalone blast using qcovs:

    blastn -task megablast -db nt -query seqs.fasta -max_target_seqs 5 -outfmt "7 std qcovs"

    All the other outputs seem to be fine, but I cannot get query coverage output:

    # BLASTN 2.2.26+
    # Query: comp2_c0_seq1 len=213 path=[905:0-58 1657:59-212]
    # Database: /nfs/ffeng-lab-data/blastDBs/nt
    # Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
    # 5 hits found
    comp2_c0_seq1 gi|325197263|gb|AC241982.2| 94.76 210 11 0 1210 1947 1738 2e-86 327
    comp2_c0_seq1 gi|212374812|gb|AC217674.3| 94.29 210 12 0 1210 27303 27094 8e-85 322
    comp2_c0_seq1 gi|209915647|gb|AC194652.4| 94.29 210 12 0 1210 134086 133877 8e-85 322
    comp2_c0_seq1 gi|156255299|gb|AC199643.3| 94.29 210 12 0 1210 52769 52560 8e-85 322
    comp2_c0_seq1 gi|155029613|gb|AC199644.3| 94.29 210 12 0 1210 91737 91528 8e-85 322


    Any suggesions? thanks

  • #2
    BLAST 2.2.28+ was the first release with support for custom tabular output with query coverage.

    edit. 2.2.29+ was apparently released a few days ago
    Last edited by rhinoceros; 01-20-2014, 11:49 AM.
    savetherhino.org

    Comment


    • #3
      that would make sense

      i will get the newer version

      thanks!

      Comment

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