no qcovs output from standalone blast

[spaceace507]

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

[rhinoceros]

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

[spaceace507]

that would make sense

i will get the newer version

thanks!