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annotate uniqprimer-0.5.0/logfile @ 5:e57b034c1fae draft

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author dereeper
date Mon, 03 Jan 2022 10:07:20 +0000
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1 utils::Initialize( ) - Initialization complete. Temporary directory: tmpFDxzqF
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2 uniqprimer::Main( ) - Logging include files:
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3 uniqprimer::Main( ) - data/X11-5Agenome.fasta
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4 uniqprimer::Main( ) - Logging exclude files:
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5 uniqprimer::Main( ) - data/XCCgenome.fasta
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6 UniqPrimerFinder::__init__() - Initializing UniqPrimerFinder
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7 utils::search_file - Path: /SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/tmp/8261175.1.bioinfo.q:/SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/usr/lib64/qt-3.3/bin::/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin
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8 utils::search_file - Path: /SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/tmp/8261175.1.bioinfo.q:/SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/usr/lib64/qt-3.3/bin::/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin
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9 utils::search_file - Path: /SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/tmp/8261175.1.bioinfo.q:/SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/usr/lib64/qt-3.3/bin::/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin
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10 utils::search_file - Path: /SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/tmp/8261175.1.bioinfo.q:/SATA/bioinfo/galaxy/galaxy_env/bin:/usr/local/bioinfo/galaxy/galaxy-python:/SGE/n1ge62/bin/lx24-amd64:/usr/lib64/qt-3.3/bin::/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin:/usr/local/bioinfo/bin:/usr/local/bioinfo/abyss/bin:/usr/local/bioinfo/al2co:/usr/local/bioinfo/amos/bin:/usr/local/bioinfo/bambus/bin:/usr/local/bioinfo/bedtools/bin:/usr/local/bioinfo/bimbam:/usr/local/bioinfo/blast/bin:/usr/local/bioinfo/blast+/bin:/usr/local/bioinfo/bowtie:/usr/local/bioinfo/bowtie2:/usr/local/bioinfo/bwa:/usr/local/bioinfo/caftools/bin:/usr/local/bioinfo/CAP3:/usr/local/bioinfo/carthagene:/usr/local/bioinfo/cdhit:/usr/local/bioinfo/censor/bin:/usr/local/bioinfo/clustalw:/usr/local/bioinfo/consed/bin:/usr/local/bioinfo/cross_match:/usr/local/bioinfo/cufflinks:/usr/local/bioinfo/decoder:/usr/local/bioinfo/dssp:/usr/local/bioinfo/EIG3.0/bin:/usr/local/bioinfo/EMBOSS/bin:/usr/local/bioinfo/ESTScan:/usr/local/bioinfo/eval:/usr/local/bioinfo/eugene-3.2/bin:/usr/local/bioinfo/eugene-3.5g/bin:/usr/local/bioinfo/exonerate/bin:/usr/local/bioinfo/FastME:/usr/local/bioinfo/fastx_toolkit:/usr/local/bioinfo/flexbar:/usr/local/bioinfo/FINDMite:/usr/local/bioinfo/fpc:/usr/local/bioinfo/fpocket2:/usr/local/bioinfo/freebayes:/usr/local/bioinfo/GERP:/usr/local/bioinfo/gevalt:/usr/local/bioinfo/gnuplot/bin:/usr/local/bioinfo/GTH/bin:/usr/local/bioinfo/hmmer/bin:/usr/local/bioinfo/hcluster_sg:/usr/local/bioinfo/ImageMagick/bin:/usr/local/bioinfo/i-adhore:/usr/local/bioinfo/JimKent:/usr/local/bioinfo/LTR_BMC:/usr/local/bioinfo/LTR_FINDER:/usr/local/bioinfo/LTRharvest/bin:/usr/local/bioinfo/mafft/bin:/usr/local/bioinfo/mapmaker:/usr/local/bioinfo/MapSplice/bin:/usr/local/bioinfo/maxcluster:/usr/local/bioinfo/mcl/bin:/usr/local/bioinfo/MCQTL/bin/Linux:/usr/local/bioinfo/meme/bin:/usr/local/bioinfo/mfold_util/bin:/usr/local/bioinfo/mira/bin:/usr/local/bioinfo/mistral:/usr/local/bioinfo/modeller9v7/bin:/usr/local/bioinfo/mreps:/usr/local/bioinfo/MUMmer:/usr/local/bioinfo/MUSTANG:/usr/local/bioinfo/MultiProtInstall:/usr/local/bioinfo/multalin:/usr/local/bioinfo/muscle:/usr/local/bioinfo/paircoil2:/usr/local/bioinfo/PHYML:/usr/local/bioinfo/pals:/usr/local/bioinfo/paml/bin:/usr/local/bioinfo/phase:/usr/local/bioinfo/phred:/usr/local/bioinfo/piler:/usr/local/bioinfo/plink:/usr/local/bioinfo/polyscan:/usr/local/bioinfo/oases:/usr/local/bioinfo/prank:/usr/local/bioinfo/primer3:/usr/local/bioinfo/psipred30:/usr/local/bioinfo/Prokov/bin:/usr/local/bioinfo/qmean/bin:/usr/local/bioinfo/quicktree:/usr/local/bioinfo/R/bin:/usr/local/bioinfo/RepeatMasker:/usr/local/bioinfo/recon/bin:/usr/local/bioinfo/RepSeek/bin:/usr/local/bioinfo/REPET/bin:/usr/local/bioinfo/rnammer:/usr/local/bioinfo/scip/bin:/usr/local/bioinfo/semphy:/usr/local/bioinfo/shapeIT:/usr/local/bioinfo/signalp:/usr/local/bioinfo/SpliceMachine/bin:/usr/local/bioinfo/sratoolkit:/usr/local/bioinfo/ssaha2:/usr/local/bioinfo/sspro4/bin:/usr/local/bioinfo/staden/bin:/usr/local/bioinfo/structure:/usr/local/bioinfo/T-COFFEE/bin:/usr/local/bioinfo/TRF:/usr/local/bioinfo/tassel:/usr/local/bioinfo/tgicl:/usr/local/bioinfo/tgicl/bin:/usr/local/bioinfo/tophat:/usr/local/bioinfo/treebest:/usr/local/bioinfo/tRNAscan-SE/bin:/usr/local/bioinfo/unafold/bin:/usr/local/bioinfo/vcftools/bin:/usr/local/bioinfo/velvet:/usr/local/bioinfo/ViennaRNA/bin:/usr/local/bioinfo/wgs/bin:/usr/local/bioinfo/wublast:/usr/local/bioinfo/xslt/bin:/usr/local/bioinfo/tmhmm/bin:/usr/local/bioinfo/trinity:/usr/local/bioinfo/bpp/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe20120705/bin:/SATA/bioinfo/galaxy/galaxy_dist/tools/idfixe/bin:.:/opt/IBM_DS/jre/bin
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11 UniqPrimerFinder::__init__() - Initializing UniqPrimerFinder - complete
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12 UniqPrimerFinder::findPrimers() - Finding primers for include files
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13 ExcludeFileManager::addExcludeFile( ) - adding exclude file data/XCCgenome.fasta
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14 ExcludeFileManager::exportSequences( ) - parsing exclude sequences
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15 fastaparser::parseFastaFile( ) - parsing fasta file data/XCCgenome.fasta
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16 ExcludeFileManager::exportSequences( ) - finished parsing, writing to a common file
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17 ExcludeFileManager::buildOutputFileName( ) - exclude file: tmpFDxzqF/combined_exlude.ffn
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18 ExcludeFileManager::exportSequences( ) - All sequences exported
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19 IncludeFileManager::setExcludeFile( ) - fileName tmpFDxzqF/combined_exlude.ffn
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20 IncludeFileManager::processIncludeFile( ) - processing data/X11-5Agenome.fasta
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21 IncludeFileManager::processIncludeFile( ) - running nucmer for reference file: data/X11-5Agenome.fasta
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22 IncludeFileManager::findUniqueSequence( ) - running nucmer for reference file: data/X11-5Agenome.fasta
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23 ProgramBase::Execute( ) - Running the nucmer program.
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24 ProgramBase::Execute( ) - /usr/local/bioinfo/MUMmer/nucmer -p nucmer_alignments -o --minmatch 300 --maxgap 1 data/X11-5Agenome.fasta tmpFDxzqF/combined_exlude.ffn
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25 NucmerParser::parseCoordMatchFile( ) - Parse nucmer_alignments.coords, finding 2 matches
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26 fastaparser::parseFastaFileAsPrimerSequence( ) - parsing fasta file data/X11-5Agenome.fasta
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27 fastaparser::parseFastaFileAsPrimerSequence( ) - read 1 sequences
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28 PrimerSequence::getNonMatchedSubSequences( ) - finding valid sub sequences for X11-5A
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29 PrimerSequence::findValidIndices( ) - getting unmatched sequence indices
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30 PrimerSequence::findValidIndices( ) - there are 2 excluded sequences for X11-5A
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31 PrimerSequence::findValidIndices( ) - removing exclude sequence 1958030 - 1963613
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32 PrimerSequence::findValidIndices( ) - removing exclude sequence 1958145 - 1963613
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33 PrimerSequence::findValidIndices( ) - 4341162 unique indices
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34 PrimerSequence::findValidIndexSequences( ) - getting sequences from unique indices
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35 PrimerSequence::findValidIndexSequences( ) - 2 sequences found
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36 PrimerManager::getCommonPrimers - finding primers that are common to all include files
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37 PrimerManager::findPrimer(s ) - writing sequences to a fasta file
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38 PrimerManager::writeFastaFile( ) - Writing 2 sequences to fasta file
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39 PrimerManager::writeFastaFile( ) - writing fasta file complete
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40 PrimerManager::findPrimers( ) - executing eprimer3 program
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41 ProgramBase::Execute( ) - Running the EPrimer3 program.
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42 ProgramBase::Execute( ) - /usr/local/bioinfo/EMBOSS/bin/eprimer3 tmpFDxzqF/sequenceForEprimer.fasta tmpFDxzqF/referenceprimers.ep3 -numreturn 2 -prange 300-400 -osize 20 -minsize 18 -maxsize 27
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43 PrimerManager::findPrimer( ) - eprimer3 file tmpFDxzqF/referenceprimers.ep3 created. Parsing for primers.
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44 eprimerparser::parsePrimerSequences( ) - parsing for primer sequences
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45 eprimerparser::parsePrimerSequences( ) - finished parsing. found 4 primers
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46 PrimerManager::findPrimers( ) - parsing for sequences complete
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47 UniqPrimerFinder::findPrimers( ) - found 4 unique sequences
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48 UniqPrimerFinder::writeOutputFile() - output file written.
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49 UniqPrimerFinder::findPrimers() - Finished finding primers