NAME - Run TENest in batch mode


This documentation refers to program version $Rev: 564 $


Usage -i indir -o outdir

Required Arguments

    -i,--indir         # Dir containing fasta files to process 
    -o,--outdir        # Dir to place the output in


Runs the program TE Nest in batch mode. This will run TE Nest for all fasta files located in the input directory.



Path to the directory containing the input files to annotate with TEnest. These files must be in the fasta format.


Path to the base output directory to place the output.



The organism database to use. The default organism database is maize.


The directory for wu blast. If this directory is not specified at the command line, will assume that this is at /usr/local/genome/wu_blast/


The directory that the TE Nest program is located in. If this directory is not specified, will assume that the TE Nest program is locate in your home directory at $HOME/apps/te_nest/


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.


Run the program with minimal output.

DIAGNOSTICS does not exist at: /some/directory/

The program does not exist at the directory you specified or in the directory that the program assumes it to be in. The best way to make sure this works is to specify a directory using the --tenest-dir option.

Can't open directory: /your/input/directory/

The input directory that you specified by the -i file has either been typed in incorrectly, the path you entered does not exist, or you do not have read access to that directory.

ERROR: No fasta files were found in the input directory

Currently this program assumes that all fasta files end with the fasta or fa extension. It is possible that you have fasta files in the input directory, but they do not have the *.fasta or *.fa file names.


This program does not make use of configuration files or variables set in the user environment.


Required Software

TE Nest

This program requires the installation of TE Nest. This program is available from:

Required Databases

This program requires an organism database is the TE Nest format. This databases are downloadable from:





This 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.


GNU General Public License, Version 3


James C. Estill <JamesEstill at>


STARTED: 09/29/2008

UPDATED: 03/24/2009

VERSION: $Rev: 564 $