---
RunDate: 03/28/2015
assemblyQcResults:
  spades:
    contigGcBin:
      - 20:
          - NODE_4_length_2142_cov_2.94777_ID_7
      - 25:
          - NODE_1_length_25215_cov_356.884_ID_1
          - NODE_2_length_13644_cov_8.56995_ID_3
      - 30:
          - NODE_3_length_4577_cov_4.89496_ID_5
    contigGcBinSize: 5
    contigGcPlot: contig_gc/contig_gc.png
    contigMegablast:
      counts:
        JGIContaminants.fa:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        LSSURef_119_tax_silva.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        LSURef_119_tax_silva.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        SSURef_119_tax_silva.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        green_genes16s.insa_gg16S.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        nt:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.fungi:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.microbial:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.mitochondrion:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.plant:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.plasmid:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        refseq.viral:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        sagtaminants.fa:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
      numContigs: 4
      topContigHits: {}
    contigTaxGcPlot:
      - Kingdom: megan/contigs_Kingdom.png
      - Phylum: megan/contigs_Phylum.png
      - Class: megan/contigs_Class.png
      - Order: megan/contigs_Order.png
      - Family: megan/contigs_Family.png
      - Genus: megan/contigs_Genus.png
      - Species: megan/contigs_Species.png
    contigTaxGcPlotAligner: LAST
    contigTaxGcPlotNoTotal:
      - Kingdom: megan/contigs_nototal_Kingdom.png
      - Phylum: megan/contigs_nototal_Phylum.png
      - Class: megan/contigs_nototal_Class.png
      - Order: megan/contigs_nototal_Order.png
      - Family: megan/contigs_nototal_Family.png
      - Genus: megan/contigs_nototal_Genus.png
      - Species: megan/contigs_nototal_Species.png
    gcCovTaxPlot:
      megablast:
        legend:
          - Kingdom: gc_cov/gc_cov_Kingdom.png
          - Phylum: gc_cov/gc_cov_Phylum.png
          - Class: gc_cov/gc_cov_Class.png
          - Order: gc_cov/gc_cov_Order.png
          - Family: gc_cov/gc_cov_Family.png
          - Genus: gc_cov/gc_cov_Genus.png
          - Species: gc_cov/gc_cov_Species.png
        nolegend:
          - Kingdom: gc_cov/gc_cov_Kingdom_nolegend.png
          - Phylum: gc_cov/gc_cov_Phylum_nolegend.png
          - Class: gc_cov/gc_cov_Class_nolegend.png
          - Order: gc_cov/gc_cov_Order_nolegend.png
          - Family: gc_cov/gc_cov_Family_nolegend.png
          - Genus: gc_cov/gc_cov_Genus_nolegend.png
          - Species: gc_cov/gc_cov_Species_nolegend.png
      scaffold:
        gc_vs_cov_multi: gc_cov/cov/scaffolds_2k_gc_cov_nolegend.png
    ncbiScreening:
      - No contaminants found:
          alignLength: ''
          hit: ''
          pctId: ''
    singleCopyGene:
      archaea:
        estGenomeRecovery: 0
        geneList:
          IF-2: 0
          RNA_pol_A_bac: 0
          RNA_pol_Rpb1_1: 0
          RNA_pol_Rpb1_2: 0
          RNA_pol_Rpb1_3: 0
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb2_1: 0
          RNA_pol_Rpb2_2: 0
          RNA_pol_Rpb2_3: 0
          RNA_pol_Rpb2_6: 0
          RNA_pol_Rpb2_7: 0
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L13: 0
          Ribosomal_L14: 0
          Ribosomal_L16: 0
          Ribosomal_L18p: 0
          Ribosomal_L2: 0
          Ribosomal_L22: 0
          Ribosomal_L23: 0
          Ribosomal_L29: 0
          Ribosomal_L2_C: 0
          Ribosomal_L3: 0
          Ribosomal_L4: 0
          Ribosomal_L5: 0
          Ribosomal_L5_C: 0
          Ribosomal_L6: 0
          Ribosomal_S11: 0
          Ribosomal_S12: 0
          Ribosomal_S13: 0
          Ribosomal_S15: 0
          Ribosomal_S17: 0
          Ribosomal_S19: 0
          Ribosomal_S2: 0
          Ribosomal_S3_C: 0
          Ribosomal_S5: 0
          Ribosomal_S5_C: 0
          Ribosomal_S7: 0
          Ribosomal_S8: 0
          Ribosomal_S9: 0
          SecY: 0
        histogram:
          0: 43
        plot:
          gene: single_copy_gene/archaea/genes.pdf
          histogram: single_copy_gene/archaea/hist.png
          outlier: single_copy_gene/archaea/outliers.png
      bacteria:
        estGenomeRecovery: 1.48
        geneList:
          DNA_pol3_beta: 0
          DNA_pol3_beta_2: 0
          DNA_pol3_beta_3: 0
          EF_TS: 0
          GTP1_OBG: 0
          IF-2: 0
          IF2_N: 0
          IF3_C: 0
          IF3_N: 0
          RNA_pol_A_CTD: 0
          RNA_pol_A_bac: 0
          RNA_pol_L: 0
          RNA_pol_Rpb1_1: 0
          RNA_pol_Rpb1_2: 0
          RNA_pol_Rpb1_3: 0
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb1_5: 0
          RNA_pol_Rpb2_1: 0
          RNA_pol_Rpb2_2: 0
          RNA_pol_Rpb2_3: 0
          RNA_pol_Rpb2_45: 0
          RNA_pol_Rpb2_6: 0
          RNA_pol_Rpb2_7: 0
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L12: 0
          Ribosomal_L13: 0
          Ribosomal_L14: 0
          Ribosomal_L16: 0
          Ribosomal_L17: 0
          Ribosomal_L18e: 0
          Ribosomal_L18p: 0
          Ribosomal_L19: 0
          Ribosomal_L2: 0
          Ribosomal_L20: 0
          Ribosomal_L21p: 0
          Ribosomal_L22: 0
          Ribosomal_L23: 0
          Ribosomal_L27: 0
          Ribosomal_L28: 0
          Ribosomal_L29: 0
          Ribosomal_L2_C: 0
          Ribosomal_L3: 0
          Ribosomal_L32p: 0
          Ribosomal_L35p: 0
          Ribosomal_L4: 0
          Ribosomal_L5: 0
          Ribosomal_L5_C: 0
          Ribosomal_L6: 0
          Ribosomal_L9_C: 0
          Ribosomal_L9_N: 0
          Ribosomal_S10: 0
          Ribosomal_S11: 0
          Ribosomal_S12: 0
          Ribosomal_S13: 0
          Ribosomal_S15: 0
          Ribosomal_S16: 0
          Ribosomal_S17: 0
          Ribosomal_S19: 0
          Ribosomal_S2: 0
          Ribosomal_S20p: 0
          Ribosomal_S3_C: 0
          Ribosomal_S4: 0
          Ribosomal_S5: 0
          Ribosomal_S5_C: 0
          Ribosomal_S6: 0
          Ribosomal_S7: 0
          Ribosomal_S8: 0
          Ribosomal_S9: 0
          SecG: 0
          SecY: 0
          UPF0079: 0
          eIF-1a: 1
        histogram:
          0: 74
          1: 1
        plot:
          gene: single_copy_gene/bacteria/genes.pdf
          histogram: single_copy_gene/bacteria/hist.png
          outlier: single_copy_gene/bacteria/outliers.png
    tetramerFailureFile: tetramer/tetramer.failedCriteria
    tetramerPlot: ''
assemblyStatistics:
  spades:
    assemblerVersion: 3.0.0
    assemblyDepth: 0
    assemblyParams: -t 16 -m 120 --sc --careful --12
    contigFile: spades/contigs.2k.fasta
    exec: /usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py
    inputFastq: AAUAN.15M.bbqc.fq.gz.fastq
    metrics:
      - Assembly method: SPAdes
      - Scaffold total: 4
      - Contig total: 4
      - Scaffold sequence length: 45.6 kb
      - Contig sequence length: 45.6 kb ( 0.0% gap)
      - Scaffold N/L50: 1/25.2 kb
      - Contig N/L50: 1/25.2 kb
      - Largest Contig: 25.2 kb
      - Number of scaffolds > 50 kb: 0
      - Pct of genome in scaffolds > 50 kb: 0.0
      - Pct of reads asssembled: 96.2
    numAssembledBases: 0
    numAssembledReads: 0
    order: 1
    scaffoldFile: spades/scaffolds.2k.fasta
    statsFile: spades/stats.spades
    totalContigLength: 45578
directory:
  allpaths: allpaths
  output: /global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/AAUAN
  pe1ContamFilter: contam_filter_clip
  pe1ContamId: contam_id_clip
  stdContamFilter: contam_filter
  stdContamId: contam_id
  velvet: velvet
  velvetOptimizerDir: velvetOpt
  vpAllpaths: vpallpaths
env:
  AGP_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/agp/agp.pl
  ASSEM_16S_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/assem16s/DEFAULT/assem16s.py
  BLASTALL_EXE: /usr/common/jgi/aligners/blast/2.2.26/bin/blastall
  BLASTN_EXE: /usr/common/jgi/aligners/blast+/2.2.28/bin/blastn
  BLASTP_EXE: /usr/common/jgi/aligners/blast+/2.2.28/bin/blastp
  BLASTX_EXE: /usr/common/jgi/aligners/blast+/2.2.28/bin/blastx
  BOWTIE_BUILD_EXE: /usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie-build
  BOWTIE_EXE: /usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie
  BWA_EXE: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa
  BlASTDBCMD_EXE: /usr/common/jgi/aligners/blast+/2.2.28/bin/blastdbcmd
  COLLECT_UNIQUE_CONTIGS: /projectb/sandbox/rqc/prod/pipelines/external_tools/LANL/collectLongestUniques_20120824.pl
  FASTX_QUALITY_STATS: /usr/common/jgi/seqtools/fastx/0.0.13.2/bin/fastx_quality_stats
  FORMATDB_EXE: /usr/common/jgi/aligners/blast/2.2.26/bin/formatdb
  GNUPLOT_EXE: /usr/common/jgi/math/gnuplot/4.6.2/bin/gnuplot
  IDBA_UD_EXE: /usr/common/jgi/assemblers/idba/1.1.1/bin/idba_ud
  ILLTOCOV_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/gc_cov/20121130/bin/illToCovGcOnRef.pl
  JAVA: /usr/common/usg/languages/java/jdk/oracle/1.7.0_51_x86_64/bin/java
  KMER_FREQUENCIES_JAR: /projectb/sandbox/rqc/prod/pipelines/external_tools/tetramerK/20120823/KmerFrequencies.jar -n
  LOOKUP_TAX_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/taxMapper/20141010/lookupTax.pl
  MEGABLAST_EXE: /usr/common/jgi/aligners/blast/2.2.26/bin/megablast
  MEGAN_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/xvfb/xvfb-run -a /jgi/tools/misc_bio/MEGAN/versions/megan-3.9/MEGAN
  NCBISCREEN_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/ncbiScreening/ncbiPreScreen.pl
  PICARD_DIR: /usr/common/jgi/Modules/modulefiles/picard/1.74
  PREPARE_ALLPATHS_INPUT_EXE: /usr/common/jgi/assemblers/allpaths-lg/46652/bin/PrepareAllPathsInputs.pl
  PRODIGAL_EXE: /usr/common/jgi/annotators/prodigal/2.50/bin/prodigal
  PYTHON_EXE: /usr/common/usg/languages/python/2.7.4/bin/python
  RSCRIPT: /global/common/genepool/usg/languages/R/3.0.1/bin/Rscript
  RUN_ALLPATHSLG_EXE: /usr/common/jgi/assemblers/allpaths-lg/46652/bin/RunAllPathsLG
  R_EXE: /global/common/genepool/usg/languages/R/3.0.1/bin/R
  SAG_DECONTAM_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/sag_decontam/scd-1.3.1/bin/scd.sh
  SAMTOOLS_EXE: /usr/common/jgi/file_formats/samtools/gcc/4.6.3/20130508/bin/samtools
  SHERA_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/shera/1.0/concatReads.pl
  SHOW_KMER_BIN_R: /projectb/sandbox/rqc/prod/pipelines/external_tools/tetramerK/20120823/showKmerBin.R
  SHUFFLE_FASTQ_EXE: /usr/common/jgi/assemblers/velvet/1.2.07/bin/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl
  SPADES_EXE: /usr/common/jgi/assemblers/spades/3.0.0_1/bin/spades.py
  SUBMISSION_PREP_EXE: /usr/common/jgi/assemblers/allpaths-lg/46652/bin/SubmissionPrep
  TAXMAPPER_DB_PATH: /projectb/sandbox/rqc/qcdb/taxonomy/tax/2014.10.10
  TAXMAPPER_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/taxMapper/20141010/taxMapper.pl -strain
  VELVETG_EXE: /usr/common/jgi/assemblers/velvet/1.2.07/bin/velvetg-k97_c2
  VELVETH_EXE: /usr/common/jgi/assemblers/velvet/1.2.07/bin/velveth-k97_c2
  VELVETOPTIMIZER_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/VelvetOptimiser/v2_1_7/VelvetOptimiser2.pl
  VELVETSC: /projectb/sandbox/rqc/prod/pipelines/external_tools/LANL/velvetsc.galaxy3.pl
  WGSIM_EXE: /usr/common/jgi/file_formats/samtools/gcc/4.6.3/20130508/bin/wgsim
  XVFB_RUN: /projectb/sandbox/rqc/prod/pipelines/external_tools/xvfb/xvfb-run
  ZIP_EXE: /bin/gzip
finalAssembly:
  assemblyFile: spades/scaffolds.2k.fasta
  assemblyType: spades
  contigFileForQc: spades/contigs.2k.fasta
  inputReadFile: AAUAN.15M.bbqc.fq.gz.fastq
  scaffoldFileForQc: spades/scaffolds.2k.fasta
inputFastq:
  std: AAUAN.15M.bbqc.fq.gz.fastq
inputReadFile:
  std:
    dataType: Illumina Std PE (cassava 1.8)
    filename: AAUAN.15M.bbqc.fq.gz.fastq
    library: LIB
    numReads: 100086
    readType: 2x150
rawReadStatistics:
  footnote: A genome size of 5.0 Mbp was assumed in this calculation.
  stats:
    std:
      - Number of reads: '100,086'
      - Sequencing depth: 3X
      - Read type: 2x150 bp
report:
  estGenomeSize: 5000000
  genomeProjectStandard: Standard Draft
  label:
    type:
      - std: Illumina Std PE
      - pe1: Illumina CLIP PE
      - pe2: PacBio
  logo:
    image: /global/common/genepool/jgi/qaqc/jigsaw/2.4.1-prod_2.4.2-24-gf598c31/config/logo.jpg
    width: 22mm
  methodSection:
    assembly:
      assemblySize: 45.6 kb
      estGenomeSize: 5.0 Mb
      numContigs: 4
      numScaffolds: 4
    read:
      std:
        numRawBases: 15.0 Mb
        numRawReads: '100,086'
        rawReadLen: 150
    tool:
      spades:
        params: -t 16 -m 120 --sc --careful --12
        version: 3.0.0
  pipelineVersion: 2.4.2
  qdReport: final/QD.finalReport.txt
  sampleSizeToComputeReadType: 50000
  title: 'QD/SAG JGI SINGLE-CELL QC AND ASSEMBLY REPORT - <PROJECT_ID> <BIOCLASS_NAME>'
  workflow: sag
seqDataAvailability:
  file:
    SPAdes: contigs.2k.fasta
