---
name: "cmpress"
section: "1"
platform: "linux"
package: "infernal"
version: "1.1.5-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmpress"
---

# cmpress(1)

prepare a covariance model database for cmscan

## NAME

cmpress - prepare a covariance model database for cmscan

## SYNOPSIS

**cmpress** *\[options\]* *\<cmfile\>*

## DESCRIPTION

Starting from a CM database *\<cmfile\>* in standard Infernal-1.1 format, construct binary compressed datafiles for  **cmscan.** The  *cmpress* step is required for **cmscan** to work.

The  *\<cmfile\>* must be have already been calibrated with **cmcalibrate** for  **cmpress** to work.

Four files are created: *\<cmfile\>.i1m,* *\<cmfile\>.i1i,* *\<cmfile\>.i1f,* and *\<cmfile\>.i1p.* The  *\<cmfile\>.i1m* file contains the covariance models, associated filter p7 profile HMMs and their annotation in a binary format. The  *\<cmfile\>.i1i* file is an SSI index for the *\<cmfile\>.i1m* file. The *\<cmfile\>.i1f* file contains precomputed data structures for the fast heuristic filter (the SSV filter) for the filter p7 profile HMMs in *\<cmfile\>.* The *\<cmfile\>.i1p* file contains precomputed data structures for the rest of each profile filter p7 HMM.

*\<cmfile\>* may not be '-' (dash); running **cmpress** on a standard input stream rather than a file is not allowed.

## OPTIONS

- **-h**

  Help; print a brief reminder of command line usage and all available options.

- **-F**

  Force; overwrites any previous cmpress'ed datafiles. The default is to bitch about any existing files and ask you to delete them first.

## SEE ALSO

See  **[infernal(1)](/infernal/1.md)** for a master man page with a list of all the individual man pages for programs in the Infernal package.

For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page (http://eddylab.org/infernal/).

## COPYRIGHT

```
Copyright (C) 2023 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
```

For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the Infernal web page  (http://eddylab.org/infernal/).

## AUTHOR

```
http://eddylab.org
```