RepeatModeler (link)

version 1.08

de novo repeat family identification and modeling using RECON, RepeatScout, TRF & RMBlast [*] on blast databases formatted with BuildDatabase.

Program parameters

    The prefix name of a XDF formatted sequence database containing the
    genomic sequence to use when building repeat models. The database
    may be created with the WUBlast "xdformat" utility or with the
    RepeatModeler wrapper script "BuildXDFDatabase".

-engine <abblast|wublast|ncbi>
    The name of the search engine we are using. I.e abblast/wublast or
    ncbi (rmblast version).

-pa #
    Specify the number of shared-memory processors available to this
    program. RepeatModeler will use the processors to run BLAST searches
    in parallel. i.e on a machine with 10 cores one might use 1 core for
    the script and 9 cores for the BLAST searches by running with "-pa

-recoverDir <Previous Output Directory>
    If a run fails in the middle of processing, it may be possible
    recover some results and continue where the previous run left off.
    Simply supply the output directory where the results of the failed
    run were saved and the program will attempt to recover and continue
    the run.

Typical usage

/exports/software/repeatmodeler/RepeatModeler/RepeatModeler -database mydb -engine ncbi -pa 32

Gridengine wrapper

RepeatModeler will use more threads than defined by -pa so use nice


#$ -V
#$ -cwd
#$ -j y
#$ -o $JOB_ID.log

# define $DATADIR and $DATABASE before/when calling this script, e.g.:
#       export DATADIR=`pwd`
#       qsub -v SEQFILE=seq.fa -v DATABASE=mydb ...

mkdir -p $WORKDIR
/exports/software/repeatmodeler/RepeatModeler/BuildDatabase -engine ncbi -name $DATABASE $SEQFILE
nice -n 10 /exports/software/repeatmodeler/RepeatModeler/RepeatModeler -database $DATABASE -engine ncbi -pa $NSLOTS
rsync -a ./consensi.fa.classified $DATADIR/$SEQFILE.consensi.fa.classified

qsub command

export DATADIR=`pwd`
qsub -v SEQFILE=seq.fa -v DATABASE=mydb -pe smp 32 /path/to/

parallel qsub command

Submit a job for each .fa file in a directory, limit to 2 simultaneous jobs to avoid flooding queue.

export DATADIR=`pwd`
parallel -j 2 qsub -v SEQFILE={} -v DATABASE={.} -pe smp 32 -sync y /path/to/ ::: *.fa


[*]Alternatively ABBlast/WUBlast may be used.