---
RunDate: 07/02/2015
assemblyQcResults:
  sagDecontamination:
    contigGcBin:
      - 25:
          - AD-726-N03_NODE_2_length_30341_cov_50.3099_ID_3
      - 30:
          - AD-726-N03_NODE_1_length_38270_cov_49.2222_ID_1
          - AD-726-N03_NODE_3_length_27243_cov_50.6775_ID_5
          - AD-726-N03_NODE_4_length_25863_cov_29.115_ID_7
          - AD-726-N03_NODE_5_length_25008_cov_29.4586_ID_9
          - AD-726-N03_NODE_6_length_21852_cov_47.0142_ID_11
          - AD-726-N03_NODE_7_length_21216_cov_49.6223_ID_13
          - AD-726-N03_NODE_8_length_20067_cov_31.4642_ID_15
          - AD-726-N03_NODE_9_length_19746_cov_40.3656_ID_17
          - AD-726-N03_NODE_10_length_18766_cov_49.7266_ID_19
          - AD-726-N03_NODE_11_length_18647_cov_44.539_ID_21
          - AD-726-N03_NODE_12_length_17774_cov_46.8564_ID_23
          - AD-726-N03_NODE_13_length_13955_cov_25.2877_ID_25
          - AD-726-N03_NODE_14_length_11384_cov_50.333_ID_27
          - AD-726-N03_NODE_15_length_11133_cov_32.9269_ID_29
          - AD-726-N03_NODE_17_length_10651_cov_48.6603_ID_33
    contigGcBinSize: 5
    contigGcPlot: screen/contig_gc/contig_gc.png
    contigMegablast:
      counts:
        JGIContaminants.fa:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        LSSURef_119_tax_silva.fasta:
          parsed: 1
          pctHits: 6.2
          taxlist: 1
          tophit: 1
        LSURef_119_tax_silva.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        SSURef_119_tax_silva.fasta:
          parsed: 1
          pctHits: 6.2
          taxlist: 1
          tophit: 1
        green_genes16s.insa_gg16S.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        nt:
          parsed: 7
          pctHits: 6.2
          taxlist: 1
          tophit: 1
        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: 16
      topContigHits:
        16s:
          - AB193914_1_1558_Bacteria;Candidate_division_OD1;uncultured_bacterium:
              alignLength: 108
              contigName: AD-726-N03_NODE_3_length_27243_cov_50.6775_ID_5
              pctAlign: 0
              pctId: 96.30
    contigTaxGcPlot:
      - Kingdom: screen/megan/contigs_Kingdom.png
      - Phylum: screen/megan/contigs_Phylum.png
      - Class: screen/megan/contigs_Class.png
      - Order: screen/megan/contigs_Order.png
      - Family: screen/megan/contigs_Family.png
      - Genus: screen/megan/contigs_Genus.png
      - Species: screen/megan/contigs_Species.png
    contigTaxGcPlotAligner: LAST
    contigTaxGcPlotNoTotal:
      - Kingdom: screen/megan/contigs_nototal_Kingdom.png
      - Phylum: screen/megan/contigs_nototal_Phylum.png
      - Class: screen/megan/contigs_nototal_Class.png
      - Order: screen/megan/contigs_nototal_Order.png
      - Family: screen/megan/contigs_nototal_Family.png
      - Genus: screen/megan/contigs_nototal_Genus.png
      - Species: screen/megan/contigs_nototal_Species.png
    gcCovTaxPlot:
      megablast:
        legend: []
        nolegend: []
      scaffold:
        gc_vs_cov_multi: screen/gc_cov/sag_decontam_output_clean_fna_shreds_gc_cov_nolegend.png
    ncbiScreening:
      - No contaminants found:
          alignLength: ''
          hit: ''
          pctId: ''
    singleCopyGene:
      archaea:
        estGenomeRecovery: 85.27
        geneList:
          IF-2: 0
          RNA_pol_A_bac: 2
          RNA_pol_Rpb1_1: 1
          RNA_pol_Rpb1_2: 1
          RNA_pol_Rpb1_3: 1
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb2_1: 1
          RNA_pol_Rpb2_2: 1
          RNA_pol_Rpb2_3: 1
          RNA_pol_Rpb2_6: 1
          RNA_pol_Rpb2_7: 1
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L13: 1
          Ribosomal_L14: 2
          Ribosomal_L16: 2
          Ribosomal_L18p: 1
          Ribosomal_L2: 2
          Ribosomal_L22: 2
          Ribosomal_L23: 2
          Ribosomal_L29: 2
          Ribosomal_L2_C: 2
          Ribosomal_L3: 1
          Ribosomal_L4: 2
          Ribosomal_L5: 2
          Ribosomal_L5_C: 2
          Ribosomal_L6: 2
          Ribosomal_S11: 2
          Ribosomal_S12: 0
          Ribosomal_S13: 2
          Ribosomal_S15: 0
          Ribosomal_S17: 2
          Ribosomal_S19: 2
          Ribosomal_S2: 0
          Ribosomal_S3_C: 2
          Ribosomal_S5: 1
          Ribosomal_S5_C: 1
          Ribosomal_S7: 0
          Ribosomal_S8: 1
          Ribosomal_S9: 1
          SecY: 1
        histogram:
          0: 10
          1: 16
          2: 17
        plot:
          gene: screen/single_copy_gene/archaea/genes.pdf
          histogram: screen/single_copy_gene/archaea/hist.png
          outlier: /global/common/genepool/jgi/qaqc/jigsaw/2.5.1-prod_2.5.1_2-1-g32f068b/config/image_not_avail.jpg
      bacteria:
        estGenomeRecovery: 80
        geneList:
          DNA_pol3_beta: 1
          DNA_pol3_beta_2: 1
          DNA_pol3_beta_3: 1
          EF_TS: 0
          GTP1_OBG: 1
          IF-2: 0
          IF2_N: 0
          IF3_C: 1
          IF3_N: 1
          RNA_pol_A_CTD: 2
          RNA_pol_A_bac: 2
          RNA_pol_L: 2
          RNA_pol_Rpb1_1: 1
          RNA_pol_Rpb1_2: 1
          RNA_pol_Rpb1_3: 1
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb1_5: 1
          RNA_pol_Rpb2_1: 1
          RNA_pol_Rpb2_2: 1
          RNA_pol_Rpb2_3: 1
          RNA_pol_Rpb2_45: 1
          RNA_pol_Rpb2_6: 1
          RNA_pol_Rpb2_7: 1
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L12: 0
          Ribosomal_L13: 1
          Ribosomal_L14: 2
          Ribosomal_L16: 2
          Ribosomal_L17: 2
          Ribosomal_L18e: 1
          Ribosomal_L18p: 1
          Ribosomal_L19: 1
          Ribosomal_L2: 2
          Ribosomal_L20: 1
          Ribosomal_L21p: 0
          Ribosomal_L22: 2
          Ribosomal_L23: 2
          Ribosomal_L27: 1
          Ribosomal_L28: 0
          Ribosomal_L29: 2
          Ribosomal_L2_C: 2
          Ribosomal_L3: 1
          Ribosomal_L32p: 0
          Ribosomal_L35p: 1
          Ribosomal_L4: 2
          Ribosomal_L5: 2
          Ribosomal_L5_C: 2
          Ribosomal_L6: 2
          Ribosomal_L9_C: 1
          Ribosomal_L9_N: 1
          Ribosomal_S10: 0
          Ribosomal_S11: 2
          Ribosomal_S12: 0
          Ribosomal_S13: 2
          Ribosomal_S15: 0
          Ribosomal_S16: 1
          Ribosomal_S17: 2
          Ribosomal_S19: 2
          Ribosomal_S2: 0
          Ribosomal_S20p: 0
          Ribosomal_S3_C: 2
          Ribosomal_S4: 2
          Ribosomal_S5: 1
          Ribosomal_S5_C: 1
          Ribosomal_S6: 0
          Ribosomal_S7: 0
          Ribosomal_S8: 1
          Ribosomal_S9: 1
          SecG: 0
          SecY: 1
          UPF0079: 0
          eIF-1a: 2
        histogram:
          0: 21
          1: 32
          2: 22
        plot:
          gene: screen/single_copy_gene/bacteria/genes.pdf
          histogram: screen/single_copy_gene/bacteria/hist.png
          outlier: /global/common/genepool/jgi/qaqc/jigsaw/2.5.1-prod_2.5.1_2-1-g32f068b/config/image_not_avail.jpg
    tetramerFailureFile: ''
    tetramerPlot: screen/tetramer/tetramer.jpg
  spades:
    contigGcBin:
      - 25:
          - AD-726-N03_NODE_2_length_30341_cov_50.3099_ID_3
          - AD-726-N03_NODE_41_length_3603_cov_27.9298_ID_81
          - AD-726-N03_NODE_56_length_2383_cov_7.71649_ID_111
      - 30:
          - AD-726-N03_NODE_1_length_38270_cov_49.2222_ID_1
          - AD-726-N03_NODE_3_length_27243_cov_50.6775_ID_5
          - AD-726-N03_NODE_4_length_25863_cov_29.115_ID_7
          - AD-726-N03_NODE_5_length_25008_cov_29.4586_ID_9
          - AD-726-N03_NODE_6_length_21852_cov_47.0142_ID_11
          - AD-726-N03_NODE_7_length_21216_cov_49.6223_ID_13
          - AD-726-N03_NODE_8_length_20067_cov_31.4642_ID_15
          - AD-726-N03_NODE_9_length_19746_cov_40.3656_ID_17
          - AD-726-N03_NODE_10_length_18766_cov_49.7266_ID_19
          - AD-726-N03_NODE_11_length_18647_cov_44.539_ID_21
          - AD-726-N03_NODE_12_length_17774_cov_46.8564_ID_23
          - AD-726-N03_NODE_13_length_13955_cov_25.2877_ID_25
          - AD-726-N03_NODE_14_length_11384_cov_50.333_ID_27
          - AD-726-N03_NODE_15_length_11133_cov_32.9269_ID_29
          - AD-726-N03_NODE_16_length_10829_cov_17.1508_ID_31
          - AD-726-N03_NODE_17_length_10651_cov_48.6603_ID_33
          - AD-726-N03_NODE_18_length_9595_cov_50.929_ID_35
          - AD-726-N03_NODE_20_length_9086_cov_25.7744_ID_39
          - AD-726-N03_NODE_21_length_8887_cov_19.3616_ID_41
          - AD-726-N03_NODE_22_length_8225_cov_22.5288_ID_43
          - AD-726-N03_NODE_23_length_6721_cov_28.4088_ID_45
          - AD-726-N03_NODE_24_length_6519_cov_15.2907_ID_47
          - AD-726-N03_NODE_26_length_5863_cov_29.5348_ID_51
          - AD-726-N03_NODE_28_length_5624_cov_36.0937_ID_55
          - AD-726-N03_NODE_29_length_5391_cov_12.5199_ID_57
          - AD-726-N03_NODE_30_length_5189_cov_13.2386_ID_59
          - AD-726-N03_NODE_32_length_4574_cov_14.615_ID_63
          - AD-726-N03_NODE_35_length_3864_cov_32.3149_ID_69
          - AD-726-N03_NODE_36_length_3951_cov_9.48229_ID_71
          - AD-726-N03_NODE_37_length_3882_cov_40.0619_ID_73
          - AD-726-N03_NODE_38_length_3819_cov_11.916_ID_75
          - AD-726-N03_NODE_39_length_3612_cov_50.156_ID_77
          - AD-726-N03_NODE_40_length_3659_cov_36.7839_ID_79
          - AD-726-N03_NODE_42_length_3341_cov_10.8624_ID_83
          - AD-726-N03_NODE_43_length_3219_cov_31.2688_ID_85
          - AD-726-N03_NODE_44_length_3016_cov_7.37487_ID_87
          - AD-726-N03_NODE_48_length_2800_cov_10.3508_ID_95
          - AD-726-N03_NODE_52_length_2487_cov_9.10033_ID_103
          - AD-726-N03_NODE_53_length_2486_cov_7.44262_ID_105
          - AD-726-N03_NODE_57_length_2363_cov_7.12435_ID_113
          - AD-726-N03_NODE_58_length_2309_cov_10.3651_ID_115
          - AD-726-N03_NODE_59_length_2243_cov_9.39397_ID_117
          - AD-726-N03_NODE_61_length_2090_cov_5.86339_ID_121
          - AD-726-N03_NODE_64_length_2014_cov_18.1736_ID_127
      - 35:
          - AD-726-N03_NODE_19_length_9197_cov_28.1308_ID_37
          - AD-726-N03_NODE_25_length_6102_cov_9.18274_ID_49
          - AD-726-N03_NODE_27_length_5579_cov_32.262_ID_53
          - AD-726-N03_NODE_31_length_4913_cov_22.2977_ID_61
          - AD-726-N03_NODE_33_length_4290_cov_11.8595_ID_65
          - AD-726-N03_NODE_34_length_4270_cov_17.0641_ID_67
          - AD-726-N03_NODE_46_length_2925_cov_16.8725_ID_91
          - AD-726-N03_NODE_47_length_2916_cov_9.97029_ID_93
          - AD-726-N03_NODE_49_length_2660_cov_11.8814_ID_97
          - AD-726-N03_NODE_50_length_2534_cov_7.98507_ID_99
          - AD-726-N03_NODE_51_length_2530_cov_10.3491_ID_101
          - AD-726-N03_NODE_54_length_2472_cov_6.69135_ID_107
          - AD-726-N03_NODE_55_length_2431_cov_9.01263_ID_109
          - AD-726-N03_NODE_60_length_2145_cov_9.06842_ID_119
          - AD-726-N03_NODE_63_length_2017_cov_9.01835_ID_125
      - 40:
          - AD-726-N03_NODE_45_length_2983_cov_8.51503_ID_89
    contigGcBinSize: 5
    contigGcPlot: unscreen/contig_gc/contig_gc.png
    contigMegablast:
      counts:
        JGIContaminants.fa:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        LSSURef_119_tax_silva.fasta:
          parsed: 1
          pctHits: 1.6
          taxlist: 1
          tophit: 1
        LSURef_119_tax_silva.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        SSURef_119_tax_silva.fasta:
          parsed: 1
          pctHits: 1.6
          taxlist: 1
          tophit: 1
        green_genes16s.insa_gg16S.fasta:
          parsed: 0
          pctHits: 0.0
          taxlist: 0
          tophit: 0
        nt:
          parsed: 7
          pctHits: 1.6
          taxlist: 1
          tophit: 1
        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: 63
      topContigHits: {}
    contigTaxGcPlot:
      - Kingdom: unscreen/megan/contigs_Kingdom.png
      - Phylum: unscreen/megan/contigs_Phylum.png
      - Class: unscreen/megan/contigs_Class.png
      - Order: unscreen/megan/contigs_Order.png
      - Family: unscreen/megan/contigs_Family.png
      - Genus: unscreen/megan/contigs_Genus.png
      - Species: unscreen/megan/contigs_Species.png
    contigTaxGcPlotAligner: LAST
    contigTaxGcPlotNoTotal:
      - Kingdom: unscreen/megan/contigs_nototal_Kingdom.png
      - Phylum: unscreen/megan/contigs_nototal_Phylum.png
      - Class: unscreen/megan/contigs_nototal_Class.png
      - Order: unscreen/megan/contigs_nototal_Order.png
      - Family: unscreen/megan/contigs_nototal_Family.png
      - Genus: unscreen/megan/contigs_nototal_Genus.png
      - Species: unscreen/megan/contigs_nototal_Species.png
    gcCovTaxPlot:
      megablast:
        legend:
          - Kingdom: unscreen/gc_cov/gc_cov_Kingdom.png
          - Phylum: unscreen/gc_cov/gc_cov_Phylum.png
          - Class: unscreen/gc_cov/gc_cov_Class.png
          - Order: unscreen/gc_cov/gc_cov_Order.png
          - Family: unscreen/gc_cov/gc_cov_Family.png
          - Genus: unscreen/gc_cov/gc_cov_Genus.png
          - Species: unscreen/gc_cov/gc_cov_Species.png
        nolegend:
          - Kingdom: unscreen/gc_cov/gc_cov_Kingdom_nolegend.png
          - Phylum: unscreen/gc_cov/gc_cov_Phylum_nolegend.png
          - Class: unscreen/gc_cov/gc_cov_Class_nolegend.png
          - Order: unscreen/gc_cov/gc_cov_Order_nolegend.png
          - Family: unscreen/gc_cov/gc_cov_Family_nolegend.png
          - Genus: unscreen/gc_cov/gc_cov_Genus_nolegend.png
          - Species: unscreen/gc_cov/gc_cov_Species_nolegend.png
      scaffold:
        gc_vs_cov_multi: unscreen/gc_cov/scaffolds_2k_shreds_gc_cov_nolegend.png
    ncbiScreening:
      - No contaminants found:
          alignLength: ''
          hit: ''
          pctId: ''
    singleCopyGene:
      archaea:
        estGenomeRecovery: 87.86
        geneList:
          IF-2: 1
          RNA_pol_A_bac: 2
          RNA_pol_Rpb1_1: 1
          RNA_pol_Rpb1_2: 1
          RNA_pol_Rpb1_3: 1
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb2_1: 1
          RNA_pol_Rpb2_2: 1
          RNA_pol_Rpb2_3: 1
          RNA_pol_Rpb2_6: 1
          RNA_pol_Rpb2_7: 1
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L13: 1
          Ribosomal_L14: 2
          Ribosomal_L16: 2
          Ribosomal_L18p: 1
          Ribosomal_L2: 2
          Ribosomal_L22: 2
          Ribosomal_L23: 2
          Ribosomal_L29: 2
          Ribosomal_L2_C: 2
          Ribosomal_L3: 1
          Ribosomal_L4: 2
          Ribosomal_L5: 2
          Ribosomal_L5_C: 2
          Ribosomal_L6: 2
          Ribosomal_S11: 2
          Ribosomal_S12: 0
          Ribosomal_S13: 2
          Ribosomal_S15: 0
          Ribosomal_S17: 2
          Ribosomal_S19: 2
          Ribosomal_S2: 0
          Ribosomal_S3_C: 2
          Ribosomal_S5: 1
          Ribosomal_S5_C: 1
          Ribosomal_S7: 0
          Ribosomal_S8: 1
          Ribosomal_S9: 1
          SecY: 1
        histogram:
          0: 9
          1: 17
          2: 17
        plot:
          gene: unscreen/single_copy_gene/archaea/genes.pdf
          histogram: unscreen/single_copy_gene/archaea/hist.png
          outlier: /global/common/genepool/jgi/qaqc/jigsaw/2.5.1-prod_2.5.1_2-1-g32f068b/config/image_not_avail.jpg
      bacteria:
        estGenomeRecovery: 82.96
        geneList:
          DNA_pol3_beta: 1
          DNA_pol3_beta_2: 1
          DNA_pol3_beta_3: 1
          EF_TS: 0
          GTP1_OBG: 1
          IF-2: 1
          IF2_N: 0
          IF3_C: 1
          IF3_N: 2
          RNA_pol_A_CTD: 2
          RNA_pol_A_bac: 2
          RNA_pol_L: 2
          RNA_pol_Rpb1_1: 1
          RNA_pol_Rpb1_2: 1
          RNA_pol_Rpb1_3: 1
          RNA_pol_Rpb1_4: 0
          RNA_pol_Rpb1_5: 1
          RNA_pol_Rpb2_1: 1
          RNA_pol_Rpb2_2: 1
          RNA_pol_Rpb2_3: 1
          RNA_pol_Rpb2_45: 1
          RNA_pol_Rpb2_6: 1
          RNA_pol_Rpb2_7: 1
          Ribosomal_L1: 0
          Ribosomal_L10: 0
          Ribosomal_L11: 0
          Ribosomal_L11_N: 0
          Ribosomal_L12: 0
          Ribosomal_L13: 1
          Ribosomal_L14: 2
          Ribosomal_L16: 2
          Ribosomal_L17: 2
          Ribosomal_L18e: 1
          Ribosomal_L18p: 1
          Ribosomal_L19: 1
          Ribosomal_L2: 2
          Ribosomal_L20: 2
          Ribosomal_L21p: 0
          Ribosomal_L22: 2
          Ribosomal_L23: 2
          Ribosomal_L27: 1
          Ribosomal_L28: 0
          Ribosomal_L29: 2
          Ribosomal_L2_C: 2
          Ribosomal_L3: 1
          Ribosomal_L32p: 0
          Ribosomal_L35p: 1
          Ribosomal_L4: 2
          Ribosomal_L5: 2
          Ribosomal_L5_C: 2
          Ribosomal_L6: 2
          Ribosomal_L9_C: 1
          Ribosomal_L9_N: 1
          Ribosomal_S10: 1
          Ribosomal_S11: 2
          Ribosomal_S12: 0
          Ribosomal_S13: 2
          Ribosomal_S15: 0
          Ribosomal_S16: 1
          Ribosomal_S17: 2
          Ribosomal_S19: 2
          Ribosomal_S2: 0
          Ribosomal_S20p: 0
          Ribosomal_S3_C: 2
          Ribosomal_S4: 2
          Ribosomal_S5: 1
          Ribosomal_S5_C: 1
          Ribosomal_S6: 0
          Ribosomal_S7: 0
          Ribosomal_S8: 1
          Ribosomal_S9: 1
          SecG: 0
          SecY: 1
          UPF0079: 0
          eIF-1a: 2
        histogram:
          0: 19
          1: 32
          2: 24
        plot:
          gene: unscreen/single_copy_gene/bacteria/genes.pdf
          histogram: unscreen/single_copy_gene/bacteria/hist.png
          outlier: /global/common/genepool/jgi/qaqc/jigsaw/2.5.1-prod_2.5.1_2-1-g32f068b/config/image_not_avail.jpg
    tetramerFailureFile: ''
    tetramerPlot: unscreen/tetramer/tetramer.jpg
assemblyStatistics:
  sagDecontamination:
    contigFile: sag_decontam/sag_decontam_output_clean.fna
    inputFastq: contam_filter/AD-726-N03_pe.contam.artifact.clean.fastq
    isAssemblyModifier: 1
    metrics:
      - Assembly method: SPAdes with auto decontamination (ProDeGe)
      - Scaffold total: 16
      - Contig total: 16
      - Scaffold sequence length: 0.329 Mb
      - Contig sequence length: 0.329 Mb  	0.000% gap
      - Scaffold N/L50: 6/21.652 kb
      - Contig N/L50: 6/21.652 kb
      - Largest Contig: 38.1 kb
      - Number of scaffolds > 50 kb: 0
      - Pct of genome in scaffolds > 50 kb: 0.00
      - Pct of reads asssembled (raw): 82.7
      - Pct of reads asssembled (decontam): 79.4
    order: 2
    parentAssemblerType: spades
    scaffoldFile: sag_decontam/sag_decontam_output_clean.fna
    statsFile: sag_decontam/stats.sag_decontam
    totalContigLength: 328715
  spades:
    assemblerVersion: 3.5.0
    assemblyDepth: 0
    assemblyParams: -t 8 -m 40 --sc --careful --12
    contigFile: spades/contigs.2k.fasta
    exec: /usr/common/jgi/assemblers/spades/3.5.0/bin/spades.py
    inputFastq: contam_filter/AD-726-N03_pe.contam.artifact.clean.fastq
    metrics:
      - Assembly method: SPAdes
      - Scaffold total: 63
      - Contig total: 63
      - Scaffold sequence length: 0.523 Mb
      - Contig sequence length: 0.523 Mb  	0.000% gap
      - Scaffold N/L50: 11/18.447 kb
      - Contig N/L50: 11/18.447 kb
      - Largest Contig: 38.1 kb
      - Number of scaffolds > 50 kb: 0
      - Pct of genome in scaffolds > 50 kb: 0.00
      - Pct of reads asssembled: 82.7
    numAssembledBases: 0
    numAssembledReads: 0
    order: 1
    scaffoldFile: spades/scaffolds.2k.fasta
    statsFile: spades/stats.spades
    totalContigLength: 522925
contamFilter:
  dir:
    std: contam_filter
  files:
    std:
      configFile: /global/common/genepool/jgi/qaqc/jigsaw/2.5.1-prod_2.5.1_2-1-g32f068b/bin/../config/run_contam_filter_sag-spades.config
      fastqFile: contam_filter/AD-726-N03_pe.contam.artifact.clean.fastq
      statsFile: contam_filter/stats.contam
  stats:
    std:
      - NumReads: 8404678
      - ReadLength: 139
      - NumBases: 1168250242
      - SequenceDepth: 233.7
  tools:
    std:
      artifactRemoval:
        cmd: duk
        params: -k 22 -s 1 -c 1
      bwa:
        alnParams: ''
        sampeParams: -A -P -s
        version: 0.6.2-r126
      minPctIdForReadFiltering: 95
      normalization:
        cmd: kmernorm
        params: -k 21 -t 15 -c 2
      subsampleAfterContamFilter: 1
      subsampleSize: '20,000,000'
contamId:
  files:
    std:
      statsFile: contam_id/stats.contam
directory:
  allpaths: allpaths
  output: /global/scratch2/sd/copeland/Projects/2015/20150213-Bigelow-SAG/_Work/AD-726-N03/jigsaw-sag.Parcubacteria.AD-726-N03_pe
  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
  FASTA_STATS_EXE: /usr/common/jgi/utilities/bbtools/prod-v35.03/bin/stats.sh
  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: /global/homes/c/copeland/local/x86_64/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/prodege-2.0/bin/prodege.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/3.5.0/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: sag_decontam/sag_decontam_output_clean.fna
  assemblyType: sagDecontamination
  contigFileForQc: sag_decontam/sag_decontam_output_clean.fna
  inputReadFile: contam_filter/AD-726-N03_pe.contam.artifact.clean.fastq
  scaffoldFileForQc: sag_decontam/sag_decontam_output_clean.fna
inputFastq:
  std: AD-726-N03_pe.fastq
inputReadFile:
  std:
    dataType: Illumina Std PE (cassava 1.3)
    filename: AD-726-N03_pe.fastq
    library: LIB
    numReads: 8406756
    readType: 2x139
rawReadStatistics:
  footnote: A genome size of 5.0 Mbp was assumed in this calculation.
  stats:
    std:
      - Number of reads: '8,406,756'
      - Sequencing depth: 234X
      - Read type: 2x139 bp
readQcResults:
  contamIdHits:
    std:
      - Ralstonia:
          pctTotal: 0.00
          total: 2
  contamIdStats:
    std:
      - Input:
          pctTotal: 100
          total: '8,406,756'
      - Contam identified:
          pctTotal: 0.0
          total: 2
  contamRmStats:
    std:
      - Input:
          pctTotal: 100
          total: '8,406,756'
      - Contam removed:
          pctTotal: 0.0
          total: 0
      - Artifact removed:
          pctTotal: 0.0
          total: '2,078'
      - Total removed:
          pctTotal: 0.0
          total: '2,078'
      - Total remaining:
          pctTotal: 100.0
          total: '8,404,678'
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/2.5.1-prod_2.5.1_2-1-g32f068b/config/logo.jpg
    width: 22mm
  methodSection:
    assembly:
      assemblySize: 0.329 Mbp
      estGenomeSize: 5.0 Mbp
      numContigs: 16
      numScaffolds: 16
    read:
      std:
        filteredReadSeqDepth: 233.7
        numFilteredReadBases: '1,168.3 Mbp'
        numFilteredReads: 8.4 Mbp
        numRawBases: '1,168.5 Mbp'
        numRawReads: '8,406,756'
        rawReadLen: 139
    tool:
      sagDecontamination:
        params: ''
        version: ''
      spades:
        params: -t 8 -m 40 --sc --careful --12
        version: 3.5.0
  minScreenContigLength: 200000
  pipelineVersion: 2.5.1
  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 with auto decontamination (ProDeGe): sag_decontam_output_clean.fna
