---
name: "gt-speck"
section: "1"
platform: "linux"
package: "genometools"
version: "1.6.5+ds-2.2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gt-speck"
---

# gt-speck(1)

Checks spec definition compliance in GFF3 input.

## NAME

gt-speck - Checks spec definition compliance in GFF3 input.

## SYNOPSIS

**gt speck** \[options\] \[GFF3\_file ...\]

## DESCRIPTION

- **-specfile** \[*filename*\]

  file with specification definition (default: undefined)

- **-colored** \[*yes\|no*\]

  show colored output (default: yes)

- **-provideindex** \[*yes\|no*\]

  provide feature index in specfile namespace (requires O(n) memory for n input features) (default: no)

- **-sort** \[*yes\|no*\]

  sort input before checking (requires O(n) memory for n input features) (default: no)

- **-failhard** \[*yes\|no*\]

  stop processing and report runtime errors instead of recording them in the results (default: no)

- **-output** \[*string*\]

  output format choose from: \[json, text, html, statsonly, tabular\] or give path to output driver (default: text)

- **-typecheck** \[*string*\]

  use an ontology given in an OBO file to validate parent-child relationships. If no argument is given, the sofa.obo file from the gtdata/obo\_files directory is used. If an argument is given, it is used as an OBO filename. In the case that such a file does not exist *.obo* is added to the argument and loading the resulting filename from the gtdata/obo\_files directory is attempted. (default: so)

- **-seqfile** \[*filename*\]

  set the sequence file from which to take the sequences (default: undefined)

- **-encseq** \[*filename*\]

  set the encoded sequence indexname from which to take the sequences (default: undefined)

- **-seqfiles**

  set the sequence files from which to extract the features use *--* to terminate the list of sequence files

- **-matchdesc** \[*yes\|no*\]

  search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)

- **-matchdescstart** \[*yes\|no*\]

  exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)

- **-usedesc** \[*yes\|no*\]

  use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (*III*) and the first range position as offset (*1000001*) (default: no)

- **-regionmapping** \[*string*\]

  set file containing sequence-region to sequence file mapping (default: undefined)

- **-o** \[*filename*\]

  redirect output to specified file (default: undefined)

- **-gzip** \[*yes\|no*\]

  write gzip compressed output file (default: no)

- **-bzip2** \[*yes\|no*\]

  write bzip2 compressed output file (default: no)

- **-force** \[*yes\|no*\]

  force writing to output file (default: no)

- **-v** \[*yes\|no*\]

  be verbose (default: no)

- **-help**

  display help and exit

- **-version**

  display version information and exit

## REPORTING BUGS

Report bugs to https://github.com/genometools/genometools/issues.