3 Command line options.MD

Command line options

Commands

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.

Makedb options

• --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.

  A custom file following the same format may be supplied here. Note that the first line of this file is assumed to contain headings and will be ignored.

• --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.

General options

• --threads/-p #

  Number of CPU threads. By default, the program will auto-detect and use all available virtual cores on the machine.

• --quiet

  Disable all terminal output.

• --verbose/-v

  Enable more verbose terminal output.

• --log

  Enable even more verbose terminal output, which is also written to a file named diamond.log is the current working directory.

Input options

• --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.

Alignment options

• --mid-sensitive

  Enable the mid-sensitive mode which is between the default (fast) mode and the sensitive mode in sensitivity. Option supported since v2.0.3

  Without using any sensitivity option, the default (fast) mode will run which is designed for finding hits of >70% identity and short read alignment.

• --sensitive

  Enable the sensitive mode designed for full sensitivity for hits >40% identity.

• --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.

  Available since version 2.0.0.

• --ultra-sensitive

  Enable the ultra-sensitive mode which is yet more sensitive than the --very-sensitive mode.

  Available since version 2.0.0.

• --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

• --masking (0,1)

  DIAMOND by default applies the tantan repeat masking algorithm to the query and target sequences as described in [1]. This masking procedure increases the specificity of alignments and serves to filter out spurious hits. If this is not desired, repeat masking can be disabled using --masking 0.

• --comp-based-stats (0,1)

  Compositional bias correction of alignment scores. 0 means no score correction, 1 means compositional bias correction as described in [2]. 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.

Output options

• --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. Note that this format cannot be written to a stream output like stdout.

  • 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:

    1. Query ID

    2. NCBI taxonomy ID (0 if unclassified)

    3. 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 --top 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.

  Note that using this option reduces performance.

• --query-cover #

  Report only alignments above the given percentage of query cover.

  Note that using this option reduces performance.

• --subject-cover #

  Report only alignments above the given percentage of subject cover.

  Note that using this option reduces performance.

• --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. The FASTA sequence identifier as well as the sequence of query and target need to be identical for a hit to be deleted.

Memory & performance options

• --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 decreased for reducing memory use, as well as increased for better performance (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.

View options

• --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.

Advanced options

• --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.

• --no-ranking

  Disable ranking heuristic. Ranking refers to a heuristic that eliminates hits prior to full gapped extension. It works by establishing a tentative order on the target sequences that were hit with respect to a single query. This order is determined by ungapped extension scores at seed hits. The aligner will compute gapped Smith-Waterman extensions for chunks of targets (see --ext-chunk-size) according to the ranking order until no alignment was found for the current chunk that meets the user-specified reporting criteria.

  Setting this option disables the ranking heuristic, causing gapped extensions to be computed for all seed hits.

  Option supported since v2.0.3.

• --ext-chunk-size #

  The chunk size of target sequences used by the ranking heuristic (see above). Higher numbers improve the accuracy of the algorithm. The default is the number specified by the --max-target-seqs/-k option, rounded up to the next multiple of 32, with a minimum of 128 and a maximum of 400. When using --top, the default value is 128.

  Option supported since v2.0.3.

• --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)

• --bin #

  The number of bins for storing seed hits. Higher numbers will lead to the creation of more temporary files, reduce memory usage of the extension stage, but also slightly reduce efficiency. The default value is 16, except for the ultra-sensitive mode which uses --bin 64 by default.

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[1] Martin C. Frith; A new repeat-masking method enables specific detection of homologous sequences, Nucleic Acids Research, Volume 39, Issue 4, 1 March 2011, Page e23, https://doi.org/10.1093/nar/gkq1212

[2] 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