Development manual for vsearch 2.32.0, built from the dev branch: it describes changes that are not released yet. The manual for the current release is published separately.

NAME

vsearch --udbstats — report statistics about indexed words in a UDB database file

SYNOPSIS

vsearch --udbstats udbfile [options]

DESCRIPTION

The vsearch command --udbstats reads a UDB database file and writes statistics about its indexed words (k-mers) to the log file: the report is only produced when --log is given (without it, only the generic loading summary appears on the standard error). The report gives the distribution of word frequencies across the indexed sequences in the database.

The report has four parts: a header (word length, number of index slots, DBAccel), overall totals (database size in nucleotides, number of indexed words, and the median and mean number of sequences per word), a table of the eleven most frequent words giving each word’s index and sequence form, its number of matching sequences (Size) and the first eight of them (Row), and a histogram binning the index slots by how many sequences they match, in buckets that double in width.

Several reported fields are USEARCH header fields vsearch does not use, and are constants rather than measurements: Word ones repeats the word length, Spaced, Hashed, Coded and Stepped are always No, the Cap column is always 0, and Lower is always 0 (masking is not recorded in a UDB file, so Upper and Total both equal the nucleotide count).

Note that the number of index slots is 4 raised to the power of the word length, so the cost of this command is set by the word length rather than by the size of the database.

See vsearch-udb(5) for a description of the UDB file format.

OPTIONS

mandatory options

--udbstats udbfile
Read the UDB database udbfile and report word statistics. As UDB files cannot be read from pipes, udbfile must be a seekable file path (see vsearch-udb(5)); a pipe is rejected with an error.

secondary options

--log filename
Write messages to filename. Messages include program version, start and finish times, elapsed time, amount of memory available, maximum amount of memory consumed, number of cores and command line options, and if need be, command-specific informational messages, warnings, and errors. Messages are written in addition to the standard error, not instead of it; use --quiet to silence the standard error copy (see the --quiet entry for what it spares).
--no_progress
Suppress the gradually increasing progress indicator normally written to the standard error stderr(3).
--quiet
Suppress messages to the standard output stdout(3) and standard error stderr(3), except for warnings and error messages.

ignored options

--threads positive non-null integer
Command is not multithreaded, option has no effect (a warning is printed when more than one thread is requested).

EXAMPLES

Report word statistics for a UDB database (the report needs --log; without it the command prints only the loading summary):

vsearch \
    --udbstats db.udb \
    --log stats.log

SEE ALSO

vsearch-makeudb_usearch(1), vsearch-udb2fasta(1), vsearch-udbinfo(1), vsearch-udb(5)

CITATION

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584

REPORTING BUGS

Submit suggestions and bug-reports at https://github.com/torognes/vsearch/issues, send a pull request on https://github.com/torognes/vsearch, or compose a friendly or curmudgeont e-mail to Torbjørn Rognes (torognes@ifi.uio.no).

AVAILABILITY

Source code and binaries are available at https://github.com/torognes/vsearch.

These manual pages are also published online at https://torognes.github.io/vsearch/.

COPYRIGHT

Copyright (C) 2014-2026, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri

All rights reserved.

Contact: Torbjørn Rognes torognes@ifi.uio.no, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway

This software is dual-licensed and available under a choice of one of two licenses, either under the terms of the GNU General Public License version 3 or the BSD 2-Clause License.

GNU General Public License version 3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The BSD 2-Clause License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ACKNOWLEDGMENTS

We would like to thank the authors of the following projects for making their source code available:

  • vsearch includes code from Google’s CityHash project by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.
  • vsearch includes code derived from Tatusov and Lipman’s DUST program that is in the public domain.
  • vsearch includes public domain code written by Alexander Peslyak for the MD5 message digest algorithm.
  • vsearch includes public domain code written by Steve Reid and others for the SHA1 message digest algorithm.
  • vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark Adler.
  • vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.
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