NAME - Run the program in batch mode.


This documentation refers to program version $Rev: 557 $


Usage -i InDir -o OutDir -c Config.cfg [--gff]

Required Arguments

    --indir         # Path to the input directory of fasta files
    --outdir        # Path to the base output directory
    --config        # Config file containg paramaters
    --gff           # Produce GFF formatted output


Runs the program in batch mode. This makes use of a modified version of the program that takes changes to the LTR finding parameters at the command line.



Path of the input directory. This is the directory that contains all of the fasta files to anlayze. The fasta files should all end with the fasta extension to recognized.


Path of the output directory. This is the base directory that will hold all of the output

-c, --config

Path of the config file that contains the model options for running find_ltr. This config file is a white space delimited text file that should be in the following format.

  #1   2     3     4      5     6     7      8     9   10         |
  Def  40  1100  16000    40   100   1000   500  700   0.0000000001
  Alt  40  1100  1800     40   100   1000   500  400   0.00001

More information about this file is available under configuration and environment heading below.



Location of the program. This option can also be set in the users envrionment. See Configuration and Environment below.


Run the program with minimal output.

-v, --verbose

Run the program in verbose mode.


Produce gff formatted output of the results.


Run the program in test mode. The program will not be run, but the location of source files, binaries, will be checked and the outupt directories will be created.


Short overview of how to use program from command line.


Show program usage with summary of options.


Show program version.


Show the full program manual. This uses the perldoc command to print the POD documentation for the program.


Error messages generated by this program and possible solutions are listed below.

ERROR: No fasta files were found in the input directory

The input directory does not contain fasta files in the expected format. This could happen because you gave an incorrect path or because your sequence files do not have the expected *.fasta extension in the file name.

ERROR: Could not create the output directory

The output directory could not be created at the path you specified. This could be do to the fact that the directory that you are trying to place your base directory in does not exist, or because you do not have write permission to the directory you want to place your file in.


Configuration File

The configuration file in specifies the options for running the program. This is a white space delimited text file. All lines starting with the # symbol will be treated as comments. An example of a config file is below:

  #1   2     3     4      5     6     7      8     9   10         |
  Def  40  1100  16000    40   100   1000   500  700   0.0000000001
  Alt  40  1100  1800     40   100   1000   500  400   0.00001

These 10 columns represents the following information:

Col 1.

Base_name for the parameter set. This set name will be used to name the output file, and will be added to the output of the gff output file. DO NOT INCLUDE SPACES IN NAMES

Col 2.

Minimum Length MEM

Col 3.

Mimimum distance between MEMs

Col 4.

Maximum distance between MEMs

Col 5.

Maximu gap between MEMs

Col 6.

Minimum length of the LTR

Col 7.

Maximum length of the LTR

Col 8.

Range Bin

Col 9.

Minimum length of ORF

Col 10.

Mac E value of HMM Hit

FIND_LTR_PATH Environment

As an alternative to specifying the full path of the find_ltr program with the --fl-path option, the path of the find_ltr program can be specified in the users environment. For example in bash shell, add the following line to your .bashrc

  export FIND_LTR_PATH='/usr/local/genome/'

assuming that the program is in the /usr/local/genome/ directory.


Required Software

Required Perl Modules





The program is part of the DAWG-PAWS package of genome annotation programs. See the DAWG-PAWS web page ( ) or the Sourceforge project page ( ) for additional information about this package.


A manuscript is being submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program:

JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes.




James C. Estill <JamesEstill at>


STARTED: 09/13/2007

UPDATED: 03/24/2009

VERSION: $Rev: 557 $