#!/bin/bash -l export ASSEM_16S_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/assem16s/DEFAULT/assem16s.py export VELVETOPTIMIZER_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/VelvetOptimiser/v2_1_7/VelvetOptimiser2.pl export PICARD_DIR=/usr/common/jgi/Modules/modulefiles/picard/1.74 export AGP_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/agp/agp.pl export SHERA_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/shera/1.0/concatReads.pl export NCBISCREEN_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/ncbiScreening/ncbiPreScreen.pl export ILLTOCOV_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/illToCovGcOnRef.pl export VELVETSC=/projectb/sandbox/rqc/prod/pipelines/external_tools/LANL/velvetsc.galaxy3.pl export COLLECT_UNIQUE_CONTIGS=/projectb/sandbox/rqc/prod/pipelines/external_tools/LANL/collectLongestUniques_20120824.pl export VELVETG_EXE=/usr/common/jgi/assemblers/velvet/1.2.07/bin/velvetg-k97_c2 export VELVETH_EXE=/usr/common/jgi/assemblers/velvet/1.2.07/bin/velveth-k97_c2 export SHUFFLE_FASTQ_EXE=/usr/common/jgi/assemblers/velvet/1.2.07/bin/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl export BWA_EXE=/usr/common/jgi/aligners/bwa/0.6.2/bin/bwa export PYTHON_EXE=/usr/common/usg/languages/python/2.7.4/bin/python export WGSIM_EXE=/usr/common/jgi/file_formats/samtools/gcc/4.6.3/20130508/bin/wgsim export PREPARE_ALLPATHS_INPUT_EXE=/usr/common/jgi/assemblers/allpaths-lg/46652/bin/PrepareAllPathsInputs.pl export SUBMISSION_PREP_EXE=/usr/common/jgi/assemblers/allpaths-lg/46652/bin/SubmissionPrep export RUN_ALLPATHSLG_EXE=/usr/common/jgi/assemblers/allpaths-lg/46652/bin/RunAllPathsLG export IDBA_UD_EXE=/usr/common/jgi/assemblers/idba/1.1.1/bin/idba_ud export SPADES_EXE=/usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py export ZIP_EXE=/bin/gzip export SAG_DECONTAM_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/sag_decontam/scd-1.3.1/bin/scd.sh export R_EXE=/global/common/genepool/usg/languages/R/3.0.1/bin/R export TAXMAPPER_EXE="/projectb/sandbox/rqc/prod/pipelines/external_tools/taxMapper/20141010/taxMapper.pl -strain" export TAXMAPPER_DB_PATH=/projectb/sandbox/rqc/qcdb/taxonomy/tax/2014.10.10 export LOOKUP_TAX_EXE=/projectb/sandbox/rqc/prod/pipelines/external_tools/taxMapper/20141010/lookupTax.pl export JAVA=/usr/common/usg/languages/java/jdk/oracle/1.7.0_51_x86_64/bin/java export RSCRIPT=/global/common/genepool/usg/languages/R/3.0.1/bin/Rscript export XVFB_RUN=/projectb/sandbox/rqc/prod/pipelines/external_tools/xvfb/xvfb-run export KMER_FREQUENCIES_JAR="/projectb/sandbox/rqc/prod/pipelines/external_tools/tetramerK/20120823/KmerFrequencies.jar -n" export SHOW_KMER_BIN_R=/projectb/sandbox/rqc/prod/pipelines/external_tools/tetramerK/20120823/showKmerBin.R export MEGAN_EXE="/projectb/sandbox/rqc/prod/pipelines/external_tools/xvfb/xvfb-run -a /jgi/tools/misc_bio/MEGAN/versions/megan-3.9/MEGAN" export GNUPLOT_EXE=/usr/common/jgi/math/gnuplot/4.6.2/bin/gnuplot export FORMATDB_EXE=/usr/common/jgi/aligners/blast/2.2.26/bin/formatdb export MEGABLAST_EXE=/usr/common/jgi/aligners/blast/2.2.26/bin/megablast export BLASTALL_EXE=/usr/common/jgi/aligners/blast/2.2.26/bin/blastall export BLASTN_EXE=/usr/common/jgi/aligners/blast+/2.2.28/bin/blastn export BLASTP_EXE=/usr/common/jgi/aligners/blast+/2.2.28/bin/blastp export BLASTX_EXE=/usr/common/jgi/aligners/blast+/2.2.28/bin/blastx export BlASTDBCMD_EXE=/usr/common/jgi/aligners/blast+/2.2.28/bin/blastdbcmd export PRODIGAL_EXE=/usr/common/jgi/annotators/prodigal/2.50/bin/prodigal export FASTX_QUALITY_STATS=/usr/common/jgi/seqtools/fastx/0.0.13.2/bin/fastx_quality_stats export BOWTIE_BUILD_EXE=/usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie-build export BOWTIE_EXE=/usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie export SAMTOOLS_EXE=/usr/common/jgi/file_formats/samtools/gcc/4.6.3/20130508/bin/samtools export BOWTIE_INDEX_EXE=/usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie-build cd /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea /projectb/sandbox/rqc/prod/pipelines/external_tools/singleGeneCopy/estimateGenomeCompleteness.pl --keepTemp --header -countFile /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/singleCopyGeneList.archaea.txt /projectb/sandbox/rqc/prod/pipelines/external_tools/singleGeneCopy/data_microbe/archaea_hmms /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/spades/contigs.2k.fasta > /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/summary.archaea.txt /global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/bin/singleCopyGenePlot.py -notitle -od /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/singleCopyGeneList.archaea.txt /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/hist.png /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/outliers.png /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHZG/single_copy_gene/archaea/genes.pdf exit $?