RepeatModeler¶
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¶
-database
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
9".
-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
repeatmodeler.sh:
#!/bin/bash
#$ -V
#$ -cwd
#$ -j y
#$ -o $JOB_ID.log
# define $DATADIR and $DATABASE before/when calling this script, e.g.:
# export DATADIR=`pwd`
# qsub -v SEQFILE=seq.fa -v DATABASE=mydb ...
WORKDIR=/scratch/$USER/repeatmodeler/$JOB_ID
mkdir -p $WORKDIR
cp $DATADIR/$SEQFILE $WORKDIR
cd $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/repeatmodeler.sh
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/repeatmodeler.sh ::: *.fa