---
RunDate: 02/14/2014
assemblyContigFile:
  spades: spades/contigs.2k.fasta
assemblyInputFastqFile:
  spades: /global/projectb/scratch/aclum/gaa-691/TNON/phixscreen_jigsaw/contam_filter/TNON.7707.1.80834.ATCAC.nophix.contam.artifact.clean.norm.paired.fastq
assemblyParams:
  allpathsCsvFile: allpaths/assembly/DATA/in_libs.csv
  idbaUd: --no_local
  spades: -t 8 -m 120 --sc --careful --12
  velvetOptimizer: --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"
  velvetg: -very_clean yes -exportFiltered yes -min_contig_lgth 500 -scaffolding no -cov_cutoff 10
  velveth: 63 -shortPaired
  vpAllpathsCsvFile: vpallpaths/assembly/DATA/in_libs.csv
  wgsim: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0
assemblyQcResults:
  contigGcBin:
    - 25: 'NODE_8_length_18021_cov_22.0241_ID_120431, NODE_12_length_14630_cov_24.5598_ID_120232, NODE_16_length_8407_cov_19.6982_ID_120247, NODE_20_length_6302_cov_18.9307_ID_120137, NODE_21_length_5886_cov_18.3365_ID_120693, NODE_23_length_5268_cov_18.4523_ID_119959, NODE_29_length_4180_cov_11.9775_ID_120307, NODE_33_length_2551_cov_6.41426_ID_117215, NODE_35_length_2266_cov_16.1443_ID_120573'
    - 30: 'NODE_3_length_22900_cov_23.4759_ID_119733, NODE_11_length_14634_cov_21.6911_ID_120701, NODE_18_length_7488_cov_24.4145_ID_120321, NODE_22_length_5445_cov_9.46271_ID_120685, NODE_25_length_4944_cov_7.0045_ID_119671, NODE_26_length_4660_cov_17.2321_ID_120712, NODE_27_length_4614_cov_11.7359_ID_120267, NODE_31_length_3582_cov_32.6422_ID_120105, NODE_32_length_2574_cov_28.3581_ID_120325, NODE_34_length_2478_cov_4.43541_ID_119673'
    - 35: 'NODE_2_length_26576_cov_25.4936_ID_120425, NODE_4_length_21435_cov_26.6528_ID_120251, NODE_6_length_19469_cov_22.7138_ID_118945, NODE_9_length_16865_cov_24.4964_ID_120717, NODE_10_length_16491_cov_25.9853_ID_118631, NODE_17_length_8191_cov_20.2942_ID_120703, NODE_19_length_6597_cov_13.5167_ID_93717, NODE_28_length_4252_cov_5.47057_ID_116923, NODE_36_length_2215_cov_22.7204_ID_120215'
    - 40: 'NODE_1_length_30856_cov_25.2158_ID_120183, NODE_5_length_20031_cov_26.0875_ID_120375, NODE_7_length_19354_cov_26.4856_ID_120327, NODE_13_length_13297_cov_25.218_ID_120413, NODE_14_length_11748_cov_19.7808_ID_119929, NODE_15_length_9112_cov_9.87844_ID_120001, NODE_24_length_4990_cov_0.987437_ID_120714, NODE_30_length_4062_cov_15.9613_ID_119223'
  contigGcBinSize: 5
  contigGcPlot: contig_gc/contig_gc.png
  tetramerFailureFile: ''
  tetramerPlot: tetramer/tetramer.jpg
assemblyScaffoldsFile:
  spades: spades/scaffolds.2k.fasta
assemblyStatistics:
  - Assembly method: SPAdes
  - Scaffold total: 36
  - Contig total: 38
  - Scaffold sequence length: 376.4 kb
  - Contig sequence length: 376.4 kb ( 0.0% gap)
  - Scaffold N/L50: 9/16.9 kb
  - Contig N/L50: 9/16.9 kb
  - Largest Contig: 30.9 kb
  - Number of scaffolds > 50 kb: 0
  - Pct of genome in scaffolds > 50 kb: 0.0
assemblyStats:
  assemblyDepth: 0
  numAssembledBases: 0
  numAssembledReads: 0
assemblyStatsFile:
  spades: spades/stats.spades
assemblyVersion:
  allpaths: r46652
  idbaUd: 1.1.1
  spades: 2.4.0
  velvet: 1.2.07
  velvetOptimizer: 2.1.7
  vpAllpaths: r46652
directory:
  allpaths: allpaths
  allpathsVelvetMerge: allpaths_velvet_merge
  output: /global/projectb/scratch/aclum/gaa-691/TNON/phixscreen_jigsaw_norm
  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
  BLASTALL_EXE: /usr/common/jgi/aligners/blast/2.2.26/bin/blastall
  BOWTIE_EXE: /usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie
  BOWTIE_INDEX_EXE: /usr/common/jgi/aligners/bowtie/0.12.8/bin/bowtie-build
  BWA_EXE: /usr/common/jgi/aligners/bwa/0.6.2/bin/bwa
  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_45_x86_64/bin/java
  KMER_FREQUENCIES_JAR: /projectb/sandbox/rqc/prod/pipelines/external_tools/tetramerK/20120823/KmerFrequencies.jar -n
  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
  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/2.4.0_1/bin/spades.py
  SUBMISSION_PREP_EXE: /usr/common/jgi/assemblers/allpaths-lg/46652/bin/SubmissionPrep
  TAXMAPPER_DB_PATH: /global/projectb/sandbox/rqc/qcdb/taxonomy/tax/2012.08.20
  TAXMAPPER_EXE: /projectb/sandbox/rqc/prod/pipelines/external_tools/taxMapper/20130807/taxMapper.pl
  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/contigs.2k.fasta
  assemblyType: spades
  contigFileForQc: spades/scaffolds.2k.fasta
  scaffoldFileForQc: spades/scaffolds.2k.fasta
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
inputFastq:
  std: /global/projectb/scratch/aclum/gaa-691/TNON/phixscreen_jigsaw/contam_filter/TNON.7707.1.80834.ATCAC.nophix.contam.artifact.clean.norm.paired.fastq
inputReadFile:
  std:
    dataType: Illumina Std PE (cassava 1.8)
    filename: TNON.7707.1.80834.ATCAC.nophix.contam.artifact.clean.norm.paired.fastq
    library: LIB
    numReads: 39870
    readType: 2x251
ncbiScreening:
  - No contaminants found: '		'
rawReadStatistics:
  footnote: A genome size of 5.0 Mbp was assumed in this calculation.
  stats:
    std:
      - Number of reads: '39,870'
      - Sequencing depth: 2X
      - Read type: 2x251 bp
readQcResults:
  readTaxGcPlot:
    - Kingdom: megan/reads_Kingdom.png
    - Phylum: megan/reads_Phylum.png
    - Class: megan/reads_Class.png
    - Order: megan/reads_Order.png
    - Family: megan/reads_Family.png
    - Genus: megan/reads_Genus.png
    - Species: megan/reads_Species.png
  readTaxGcPlotNoTotal:
    - nototal_Kingdom: megan/reads_nototal_Kingdom.png
    - nototal_Phylum: megan/reads_nototal_Phylum.png
    - nototal_Class: megan/reads_nototal_Class.png
    - nototal_Order: megan/reads_nototal_Order.png
    - nototal_Family: megan/reads_nototal_Family.png
    - nototal_Genus: megan/reads_nototal_Genus.png
    - nototal_Species: megan/reads_nototal_Species.png
report:
  estGenomeSize: 5000000
  genomeProjectStandard: Standard Draft
  label:
    type:
      - std: Illumina Std PE
      - pe1: Illumina CLIP PE
      - pe2: PacBio
  logo:
    image: /global/projectb/sandbox/rqc/prod/pipelines/jigsaw/2.3.1/config/logo.jpg
    width: 22mm
  methodSection:
    assembly:
      assemblySize: 376.4 Kb
      estGenomeSize: 5.0 Mb
      numContigs: 38
      numScaffolds: 36
    read:
      std:
        numRawBases: 10.0 Mb
        numRawReads: '39,870'
        rawReadLen: 251
    tool:
      allpaths:
        version: r46652
      idba:
        params: --no_local
        version: 1.1.1
      spades:
        params: -t 8 -m 120 --sc --careful --12
        version: 2.4.0
      velvet:
        velvetgParams: -very_clean yes -exportFiltered yes -min_contig_lgth 500 -scaffolding no -cov_cutoff 10
        velvethParams: 63 -shortPaired
        version: 1.2.07
      wgsim:
        params: -e 0 -1 100 -2 100 -r 0 -R 0 -X 0
  pipelineVersion: 2.3.1
  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
singleCopyGeneEstGenomeRecovery:
  - bacteria: 4.8
  - archaea: 0
