GenomeSTRIP slow

Hi all,
Recently, I am trying to identify CNV(100k ~ 10MB) from PE data with GenomeSTRIP.
I followed the instruction http://www.broadinstitute.org/software/genomestrip/org_broadinstitute_sv_qscript_SVPreprocess.html
with the command like
classpath="${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar:${SV_DIR}/lib/gatk/Queue.jar"
java -Xmx4g -cp ${classpath} \
org.broadinstitute.gatk.queue.QCommandLine \
-S ${SV_DIR}/qscript/SVPreprocess.q \
-S ${SV_DIR}/qscript/SVQScript.q \
-cp ${classpath} \
-gatk ${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-configFile ${SV_DIR}/conf/genstrip_parameters.txt \
-R path_to_rmd_dir/reference_genome.fasta \
-I input_bam_files.list \
-md output_metadata_directory \
-run

  I only input 1 bam file. The preprocess took several hours and output some empty folders.
  I am not sure if it had been run properly, and why it is so slow.

Thanks

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