--max-target-seqs/-k #
The maximum number of target sequences per query to report alignments for (default=25).
Setting this to 0 will report all alignments that were found.
--top #
Report alignments within the given percentage range of the top alignment score for a query
(overrides --max-target-seqs option). For example, setting this to 10 will report all align-
ments whose score is at most 10% lower than the best alignment score for a query.
--range-culling
Restrict hit culling to overlapping query ranges. This feature is designed for long query DNA
sequences that may span several genes. In these cases, the default of reporting the 25 best
overall hits could cause hits to a lower scoring gene to be overshadowed. But just increasing
the number of alignments reported will bloat the output size and reduce performance.
Using this feature along with -k 25 (default), a hit will only be deleted if at least 50% of its
query range is spanned by at least 25 higher or equal scoring hits.
Using this feature along with --top 10, a hit will only be deleted if its score is more than
10% lower than that of a higher scoring hit over at least 50% of its query range.
The percentage is configurable using --range-cover. Note that this feature is currently only
available in frameshift alignment mode.
--evalue/-e #
Maximum expected value to report an alignment (default=0.001).
--min-score #
Minimum bit score to report an alignment. Setting this option will override the --evalue
parameter.

--evalue 5e-6
reczko@max:~/Elixir/metagenomics/nr$ time ../diamond/diamond blastx --evalue 5e-6 -c 2 -b5.0  --frameshift 15 --range-culling --top 10 -d nr -q /data/images/proton2/run431/R_2019_08_07_16_07_46_user_IONAS-431-GKlab-MS_SPlab_190807_GK3R288-302_SP3R1-4.SPD3_fragDNA1.IonXpress_031.fastq -f 0 -o r431SPD3matches-longreads-top10.f0.eval5e-6 -t temp1
Total time = 4328.07s
Reported 127676609 pairwise alignments, 127676680 HSPs.
1353142 queries aligned.

real	72m8.778s
user	1986m26.229s
sys	35m25.360s