Commands are issued as the first parameter on the command line and set the task to be run by the program.
makedb
Create a DIAMOND formatted reference database from a FASTA input file.
blastp
Align protein query sequences against a protein reference database.
blastx
Align translated DNA query sequences against a protein reference database.
view
Generate formatted output from DAA files.
version
Print version information.
dbinfo
Print information about a database file.
help
Print help message.
test
Run a series of test cases and verify the output against reference hashes. This command will exit with code 0
if all tests have passed and 1
otherwise. Running this command requires write access to the current working directory.
--in <file>
Path to the input protein reference database file in FASTA format (may be gzip compressed). If this parameter is omitted, the input will be read from stdin
.
--db/-d <file>
Path to the output DIAMOND database file.
--taxonmap <file>
Path to mapping file that maps NCBI protein accession numbers to taxon ids (gzip compressed). This parameter is optional and needs to be supplied in order to provide taxonomy features. The file can be downloaded from NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz.
--taxonnodes <file>
Path to the nodes.dmp
file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip.
--taxonnames <file>
Path to the names.dmp
file from the NCBI taxonomy. This parameter is optional and needs to be supplied in order to provide taxonomy features. The file is contained within this archive downloadable at NCBI: ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip.
--threads/-p #
Number of CPU threads. By default, the program will auto-detect and use all available virtual cores on the machine.
--db/-d <file>
Path to the DIAMOND database file.
--query/-q <file>
Path to the query input file in FASTA or FASTQ format (may be gzip compressed). If this parameter is omitted, the input will be read from stdin
.
--taxonlist <list>
Comma-separated list of NCBI taxonomic IDs to filter the database by. Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against. Using this option requires setting the --taxonmap
and --taxonnodes
parameters for makedb
.
--query-gencode #
Genetic code used for translation of query in BLASTX mode. A list of possible values can be found at the NCBI website. By default, the Standard Code is used. Note: changing the genetic code is currently not fully supported for the DAA format.
--strand {both, plus, minus}
Set strand of query to align for translated searches. By default both strands are searched.
--min-orf/-l #
Ignore translated sequences that do not contain an open reading frame of at least this length. By default this feature is disabled for sequences of length below 30, set to 20 for sequences of length below 100, and set to 40 otherwise. Setting this option to 1
will disable this feature.
--sensitive
Enable the sensitive mode designed for full sensitivity for hits >40% identity.
Without using any sensitivity option, the default (fast) mode will run which is designed for finding hits of >70% identity and short read alignment.
--more-sensitive
This mode is slightly more sensitive than the --sensitive
mode.
--very-sensitive
Enable the very-sensitive mode designed for best sensitivity including the twilight zone range of <40% identity.
--ultra-sensitive
Enable the ultra-sensitive mode which is yet more sensitive than the --very-sensitive
mode.
--frameshift/-F #
Penalty for frameshifts in DNA-vs-protein alignments. Values around 15 are reasonable for this parameter. Enabling this feature will have the aligner tolerate missing bases in DNA sequences and is most recommended for long, error-prone sequences like MinION reads.
In the pairwise output format, frameshifts will be indicated by \
and /
for a shift by +1 and -1 nucleotide in the direction of translation respectively.
Note that this feature is disabled by default.
--gapopen #
Gap open penalty.
--gapextend #
Gap extension penalty.
--matrix <matrix name>
Scoring matrix. The following matrices are supported, with the default being BLOSUM62.
Matrix | Supported values for (gap open)/(gap extend) | Default gap penalties |
---|---|---|
BLOSUM45 | (10-13)/3; (12-16)/2; (16-19)/1 | 14/2 |
BLOSUM50 | (9-13)/3; (12-16)/2; (15-19)/1 | 13/2 |
BLOSUM62 | (6-11)/2; (9-13)/1 | 11/1 |
BLOSUM80 | (6-9)/2; 13/2; 25/2; (9-11)/1 | 10/1 |
BLOSUM90 | (6-9)/2; (9-11)/1 | 10/1 |
PAM250 | (11-15)/3; (13-17)/2; (17-21)/1 | 14/2 |
PAM70 | (6-8)/2; (9-11)/1 | 10/1 |
PAM30 | (5-7)/2; (8-10)/1 | 9/1 |
--comp-based-stats (0,1)
Compositional bias correction of alignment scores. 0 means no score correction, 1 means compositional bias correction as described in [1]. Compositionally biased sequences often cause false positive matches, which are effectively filtered by this algorithm in a way similar to the composition based statistics used by BLAST .
--algo (0,1)
Algorithm for seed search. 0 means double-indexed and 1 means query-indexed. The double-indexed algorithm is the program’s main algorithm, but it is inefficient for very small query files, where the query-indexed algorithm should be used instead.
By default, the program will automatically choose one of the algorithms based on the size of the query and database files. The algorithm used will be displayed at program startup.
Note that while the two algorithms are configured to provide roughly the same sensitivity for the respective modes, results will not be exactly identical to each other.
--out/-o <file>
Path to the output file. If this parameter is omitted, the results will be written to the standard output and all other program output will be suppressed.
--outfmt/-f #
Format of the output file. The following values are accepted:
0
BLAST pairwise format.
5
BLAST XML format.
6
BLAST tabular format (default). This format can be customized, the 6
may be followed by a space-separated list of the following keywords, each specifying a field of the output.
qseqid
Query Seq - id
qlen
Query sequence length
sseqid
Subject Seq - id
sallseqid
All subject Seq - id(s), separated by a ’;’
slen
Subject sequence length
qstart
Start of alignment in query*
qend
End of alignment in query*
sstart
Start of alignment in subject*
send
End of alignment in subject*
qseq
Aligned part of query sequence*
full_qseq
Full query sequence
sseq
Aligned part of subject sequence*
full_sseq
Full subject sequence
evalue
Expect value
bitscore
Bit score
score
Raw score
length
Alignment length*
pident
Percentage of identical matches*
nident
Number of identical matches*
mismatch
Number of mismatches*
positive
Number of positive - scoring matches*
gapopen
Number of gap openings*
gaps
Total number of gaps*
ppos
Percentage of positive - scoring matches*
qframe
Query frame
btop
Blast traceback operations(BTOP)*
cigar
CIGAR string*
staxids
Unique Subject Taxonomy ID(s), separated by a ’;’ (in numerical order). This field requires setting the --taxonmap
parameter for makedb
.
sscinames
Unique Subject Scientific Name(s), separated by a ‘;’. This field requires setting the --taxonmap
and --taxonnames
parameters for makedb
.
sskingdoms
Unique Subject Super Kingdom(s), separated by a ‘;’. This field requires setting the --taxonmap
, --taxonnodes
and --taxonnames
parameters for makedb
.
skingdoms
Unique Subject Kingdom(s), separated by a ‘;’. This field requires setting the --taxonmap
, --taxonnodes
and --taxonnames
parameters for makedb
.
sphylums
Unique Subject Phylums(s), separated by a ‘;’. This field requires setting the --taxonmap
, --taxonnodes
and --taxonnames
parameters for makedb
.
stitle
Subject Title
salltitles
All Subject Title(s), separated by a ’<>’
qcovhsp
Query Coverage Per HSP*
scovhsp
Subject Coverage Per HSP*
qtitle
Query title
qqual
Query quality values for the aligned part of the query*
full_qqual
Query quality values
qstrand
Query strand
By default, there are 12 preconfigured fields: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
.
*These fields require alignment traceback. If none of these fields are selected, traceback computation will be disabled, which improves performance and reduces use of temporary disk space.
100
DIAMOND alignment archive (DAA). The DAA format is a proprietary binary format that can subsequently be used to generate other output formats using the view
command. It is also supported by MEGAN and allows a quick import of results.
101
SAM format.
102
Taxonomic classification. This format will not print alignments but only a taxonomic classification for each query using the LCA algorithm. The output lines consist of 3 tab-delimited fields:
Query ID
NCBI taxonomy ID (0 if unclassified)
E-value of the best alignment with a known taxonomic ID found for the query (0 if unclassified)
The score range for the LCA algorithm is set by the --top
parameter. The default value is 10 which means that all alignments whose score is at most 10% lower than the best score are considered for the LCA computation.
Using this format requires setting the --taxonmap
and --taxonnodes
parameters for makedb
.
103
PAF format. The custom fields in the format are AS (bit score), ZR (raw score) and ZE (e-value).
--salltitles
Include full length subject titles into the DAA format. By default, DAA files contain only the shortened sequence id (up to the first blank character).
--sallseqid
Include all subject ids into the DAA file. By default only the first id of each subject is included. As the subject ids are much shorter than the full titles this option will save space compared to the --salltitles
option.
--compress (0,1)
Enable compression of the output file. 0 (default) means no compression, 1 means gzip compression.
--max-target-seqs/-k #
The maximum number of target sequences per query to report alignments for (default=25). Setting this to -k0
will report all targets for which alignments were found.
Note that this parameter does not only affect the reporting, but also the algorithm as it is taken into account for heuristics that eliminate hits prior to full gapped extension.
--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 alignments whose score is at most 10% lower than the best alignment score for a query.
Note that this parameter does not only affect the reporting, but also the algorithm as it is taken into account for heuristics that eliminate hits prior to full gapped extension.
--max-hsps #
The maximum number of HSPs (High-Scoring Segment Pairs) per target sequence to report for each query. The default policy is to report only the highest-scoring HSP for each target, while disregarding alternative, lower-scoring HSPs that are contained in the same target. This is not to be confused with the --max-target-seqs
option.
This parameter can be increased to report an alternative HSP if its query and subject ranges are not enveloped by a higher scoring HSP and if it meets the e-value threshold. Setting this option to --max-hsps 0
will report all alternative HSPs.
--range-culling
Enable hit culling with respect to the query range. This feature is designed for long query DNA sequences that may span several genes. In these cases, reporting the overall top N hits can cause hits to a lower-scoring gene to be superseded by a higher-scoring gene. Using this option, hit culling will be performed locally with respect to a hit’s query range, thus reporting the locally top N hits while allowing more hits that span a different region of the query.
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 overlap 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.
--id #
Report only alignments above the given percentage of sequence identity.
--query-cover #
Report only alignments above the given percentage of query cover.
--subject-cover #
Report only alignments above the given percentage of subject cover.
--unal (0,1)
Report unaligned queries (0=no, 1=yes). By default, unaligned queries are reported for the BLAST pairwise, BLAST XML and SAM format.
--no-self-hits
Suppress reporting of identical self-hits between sequences.
--block-size/-b #
Block size in billions of sequence letters to be processed at a time. This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance. The program can be expected to use roughly six times this number of memory (in GB).
The default value is -b2.0
. The parameter can be increased for better performance but values of >20 are not recommended.
The very-sensitive and ultra-sensitive modes use -b0.4
as a default. Note that these two modes benefit only slightly from increasing this parameter.
Note that this parameter affects the algorithm and results will not be completely identical for different values of the block size.
--tmpdir/-t <directory>
Directory to be used for temporary storage. This is set to the output directory by default. The amount of disk space that will be used depends on the program’s settings and the input data. As a general rule it should be ensured that 100 GB of disk space are available here.
If the program is being run in a cluster environment, and disk space is mounted over a network based file system, it is recommended to set this parameter to a fast local disk or to /dev/shm
to avoid any I/O bottlenecks.
--index-chunks/-c #
The number of chunks for processing the seed index. This option can be additionally used to tune the performance. The default value is -c4
, while setting this parameter to -c1
instead will improve the performance at the cost of increased memory use. Note that the very-sensitive and ultra-sensitive modes use -c1
by default.
--daa/-a <file>
Path to input file in DAA format.
--out/-o <file>
Path to output file. If this parameter is omitted, the results will be written to the standard output and all other program output will be suppressed.
These aligner parameters apply to the view command as well and work in the same way: --outfmt
, --compress
, --max-target-seqs
, --top
. Note that taxonomy features are currently not available for the DAA format.
--freq-sd #
During the seed search, seeds with very high frequency in the queries or the database are ignored. This option sets the number of standard deviations above the average frequency for ignoring a seed. The default values are 50 in default mode, 20 in sensitive mode, 200 in more-sensitive mode, 15 in very-sensitive mode and 20 in ultra-sensitive mode.
--ext (banded-fast,banded-slow)
This option determines how band sizes are setup for banded Smith-Waterman extension. The banded-slow
setting is slightly slower but more accurate. The defaults are banded-fast
for the default and sensitive modes, and banded-slow
for the more-sensitive, very-sensitive and ultra-sensitive modes.
--band #
Set a fixed band size for banded Smith Waterman extension. Setting this option overrides the preconfigured defaults set by the --ext
option. Note that the band size is first determined by chaining, while this parameter provides an additional band margin in both directions.
--xml-blord-format
Use gnlBL_ORD_ID style format for hit IDs in XML output.
--range-cover #
The minimum percentage of a hit’s query range that needs to be spanned by higher scoring hits for a hit to be deleted in range culling mode (default=50.0
).
--culling-overlap #
The minimum percentage of a hit’s query or target range that needs to be spanned by a higher scoring hit against the same target for a hit to be deleted. (default=50.0
)
[1] Maria Hauser, Martin Steinegger, Johannes Söding; MMseqs software suite for fast and deep clustering and searching of large protein sequence sets, Bioinformatics, Volume 32, Issue 9, 1 May 2016, Pages 1323–1330