diff test-data/PRIME/gene2.json @ 0:dd2d60b55e0d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip commit 15c654c3d27df68a47483031961ace7f5b8d998d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PRIME/gene2.json	Thu Dec 04 15:05:26 2025 +0000
@@ -0,0 +1,791 @@
+{
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+      [5.24043352637176, 0.0004338156767874127, 5.20859751191156, 0.0004338156767874127, 0.1357666032748778, 0, 1, -5.894933720870095, -5.895005662002102, 0.9999999999867918, 1, 0.886606480448811, 1, -5.894957967156203, 6.632621509002536, 1, -5.894956725977382, 14.18143511951259, 1, -5.894958091629903, 14.18143511951259, 1, -5.894956502696569, 14.18143511951259, 1, -5.894957058566754],
+      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+      [5.24043352637176, 0.0004338156767874127, 5.20859751191156, 0.0004338156767874127, 0.1357666032748778, 0, 1, -5.894933720870095, -5.895005662002102, 0.9999999999867918, 1, 0.886606480448811, 1, -5.894957967156203, 6.632621509002536, 1, -5.894956725977382, 14.18143511951259, 1, -5.894958091629903, 14.18143511951259, 1, -5.894956502696569, 14.18143511951259, 1, -5.894957058566754],
+      [7.737689682919324, 0.0002059368534316897, 7.796546118142354, 0.0002059368534316897, 0.200464301315868, 0, 1, -5.185312974623315, -5.185375021116818, 0.9999999999908757, 1, 1.697672244826404, 1, -5.185319913350097, 0.639872503016355, 1, -5.185320726580621, 14.42273103529203, 1, -5.185322382170208, 14.42273103529203, 1, -5.185318999805737, 14.67233899949953, 1, -5.185320891586968],
+      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0],
+      [0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0]
+      ]
+    },
+   "headers":    [
+["α", "Synonymous substitution rate at a site"],
+    ["β", "Property independent non-synonymous rate a site"],
+    ["FEL α", "Synonymous substitution rate at a site (FEL model)"],
+    ["FEL β", "Log of property independent non-synonymous rate a site"],
+    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
+    ["# subs", "The number of amino-acid substitutions that occurred at this site"],
+    ["# aa", "The number of unique amino-acids occurring at that site"],
+    ["PRIME LogL", "Site Log-likelihood under the PRIME model"],
+    ["FEL LogL", "Site Log-likelihood under the FEL model"],
+    ["p-value", "Omnibus q-value (any property is important)"],
+    ["q-value", "Importance for Factor I bipolar"],
+    ["λ1", "p-value for non-zero effect of Factor I bipolar"],
+    ["p1", "Log likelihood when there is no effect of Factor I bipolar"],
+    ["LogL1", "Importance for Factor II secondary structure"],
+    ["λ2", "p-value for non-zero effect of Factor II secondary structure"],
+    ["p2", "Log likelihood when there is no effect of Factor II secondary structure"],
+    ["LogL2", "Importance for Factor III volume"],
+    ["λ3", "p-value for non-zero effect of Factor III volume"],
+    ["p3", "Log likelihood when there is no effect of Factor III volume"],
+    ["LogL3", "Importance for Factor IV composition"],
+    ["λ4", "p-value for non-zero effect of Factor IV composition"],
+    ["p4", "Log likelihood when there is no effect of Factor IV composition"],
+    ["LogL4", "Importance for Factor V charge"],
+    ["λ5", "p-value for non-zero effect of Factor V charge"],
+    ["p5", "Log likelihood when there is no effect of Factor V charge"],
+    ["LogL5", "0"]
+    ],
+   "substitutions":{
+     "0":{
+       "0":null,
+       "1":null,
+       "10":null,
+       "11":null,
+       "12":null,
+       "13":null,
+       "14":null,
+       "15":null,
+       "16":null,
+       "17":null,
+       "18":null,
+       "19":null,
+       "2":null,
+       "20":null,
+       "21":null,
+       "22":null,
+       "23":null,
+       "24":null,
+       "25":{
+         "PP564823_1_2023_10_06":"GGT",
+         "root":"GTT"
+        },
+       "26":{
+         "Node2":"TCA",
+         "Node3":"CCA",
+         "PP564823_1_2023_10_06":"TCA",
+         "root":"CCA"
+        },
+       "27":null,
+       "28":null,
+       "29":null,
+       "3":null,
+       "30":null,
+       "31":null,
+       "32":null,
+       "33":null,
+       "34":{
+         "PP563831_1_2023_08_29":"GAA",
+         "root":"AAA"
+        },
+       "35":null,
+       "36":null,
+       "37":{
+         "Node8":"CTT",
+         "root":"CTC"
+        },
+       "38":null,
+       "39":null,
+       "4":{
+         "Node2":"CGG",
+         "PP564823_1_2023_10_06":"CGG",
+         "root":"CGA"
+        },
+       "40":{
+         "Node2":"CAG",
+         "root":"CAA"
+        },
+       "41":null,
+       "42":null,
+       "43":null,
+       "44":null,
+       "45":{
+         "PP564823_1_2023_10_06":"ATG",
+         "root":"CTG"
+        },
+       "46":null,
+       "47":null,
+       "48":null,
+       "49":{
+         "Node3":"TTT",
+         "root":"TTC"
+        },
+       "5":{
+         "PP564823_1_2023_10_06":"AAG",
+         "root":"AAA"
+        },
+       "50":null,
+       "51":null,
+       "52":null,
+       "53":null,
+       "54":null,
+       "55":{
+         "Node2":"TTC",
+         "root":"TTT"
+        },
+       "56":null,
+       "57":null,
+       "58":null,
+       "59":{
+         "Node3":"CCT",
+         "root":"CCC"
+        },
+       "6":null,
+       "60":null,
+       "61":null,
+       "62":null,
+       "63":{
+         "Node2":"GGG",
+         "root":"GGA"
+        },
+       "64":null,
+       "65":null,
+       "66":null,
+       "67":null,
+       "68":null,
+       "69":{
+         "Node2":"GGT",
+         "PP564823_1_2023_10_06":"AGC",
+         "root":"GGC"
+        },
+       "7":null,
+       "70":null,
+       "71":null,
+       "72":null,
+       "73":null,
+       "74":null,
+       "75":null,
+       "76":null,
+       "77":null,
+       "78":null,
+       "79":null,
+       "8":{
+         "PP564823_1_2023_10_06":"GGT",
+         "root":"GCT"
+        },
+       "80":{
+         "PP563838_1_2023_09_30":"CTG",
+         "PP564823_1_2023_10_06":"TTA",
+         "root":"CTA"
+        },
+       "81":null,
+       "82":null,
+       "83":{
+         "PP563832_1_2023_08_28":"TTT",
+         "root":"TTC"
+        },
+       "84":{
+         "PP564823_1_2023_10_06":"AAA",
+         "root":"AAG"
+        },
+       "85":null,
+       "86":{
+         "PP564823_1_2023_10_06":"GAG",
+         "root":"GAA"
+        },
+       "87":null,
+       "88":null,
+       "89":null,
+       "9":null,
+       "90":null,
+       "91":{
+         "Node2":"CTG",
+         "PP564823_1_2023_10_06":"CTG",
+         "root":"TTG"
+        },
+       "92":{
+         "PP564823_1_2023_10_06":"AAC",
+         "root":"AAT"
+        },
+       "93":null,
+       "94":null,
+       "95":{
+         "PP564823_1_2023_10_06":"AAC",
+         "root":"AAT"
+        },
+       "96":{
+         "PP564823_1_2023_10_06":"AGG",
+         "root":"AGA"
+        },
+       "97":null,
+       "98":null,
+       "99":null
+      }
+    }
+  },
+ "analysis":{
+   "authors":"Sergei L. Kosakovsky Pond",
+   "citation":"TBD",
+   "contact":"[e-mail]",
+   "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n    fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n    properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n    When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n    At each site, N tests are performed\n    A subset of branches can be selected\n    for testing as well, in which case an additional (nuisance) parameter will be\n    inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n    for recombination - aware analysis.\n    ",
+   "requirements":"in-frame codon alignment and a phylogenetic tree",
+   "residue_properties":null,
+   "version":"0.2.0"
+  },
+ "branch attributes":{
+   "0":{
+     "Node2":{
+       "Global MG94xREV":0.0155536653271895,
+       "Nucleotide GTR":0.01391650578382423
+      },
+     "Node3":{
+       "Global MG94xREV":0.007028463160179066,
+       "Nucleotide GTR":0.007313844682570613
+      },
+     "Node8":{
+       "Global MG94xREV":0.006625904948639312,
+       "Nucleotide GTR":0.006196659368038242
+      },
+     "PP563830_1_2023_09_02":{
+       "Global MG94xREV":0,
+       "Nucleotide GTR":1e-06,
+       "original name":"PP563830_1_2023_09_02"
+      },
+     "PP563831_1_2023_08_29":{
+       "Global MG94xREV":0.003308074904952416,
+       "Nucleotide GTR":0.003339882520232537,
+       "original name":"PP563831_1_2023_08_29"
+      },
+     "PP563832_1_2023_08_28":{
+       "Global MG94xREV":0.003305744077013286,
+       "Nucleotide GTR":0.003342518270787742,
+       "original name":"PP563832_1_2023_08_28"
+      },
+     "PP563838_1_2023_09_30":{
+       "Global MG94xREV":0.003316134050292535,
+       "Nucleotide GTR":0.003339882520180704,
+       "original name":"PP563838_1_2023_09_30"
+      },
+     "PP563839_1_2023_09_29":{
+       "Global MG94xREV":0,
+       "Nucleotide GTR":1e-06,
+       "original name":"PP563839_1_2023_09_29"
+      },
+     "PP563845_1_2023_10_22":{
+       "Global MG94xREV":0.005917829644775162,
+       "Nucleotide GTR":0.007157676157708746,
+       "original name":"PP563845_1_2023_10_22"
+      },
+     "PP564823_1_2023_10_06":{
+       "Global MG94xREV":0.04452770118405119,
+       "Nucleotide GTR":0.04195089101557686,
+       "original name":"PP564823_1_2023_10_06"
+      }
+    },
+   "attributes":{
+     "Global MG94xREV":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      }
+    }
+  },
+ "data partitions":{
+   "0":{
+     "coverage":      [
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
+      ],
+     "name":"prime.filter.default"
+    }
+  },
+ "fits":{
+   "Global MG94xREV":{
+     "AIC-c":1098.164186625619,
+     "Equilibrium frequencies":      [
+[0.04022787530103862],
+      [0.01934493712337751],
+      [0.03425741450905353],
+      [0.01425856648080257],
+      [0.03379960463533115],
+      [0.01625368532572285],
+      [0.0287832021345848],
+      [0.01198009852897374],
+      [0.03434841386947805],
+      [0.01651759884459136],
+      [0.02925055929127961],
+      [0.01217462118004102],
+      [0.04856425764989153],
+      [0.02335376908798366],
+      [0.04135654424169535],
+      [0.01721335494628832],
+      [0.01826098626758108],
+      [0.008781414094422619],
+      [0.01555076352482647],
+      [0.006472514015538997],
+      [0.01534294594175388],
+      [0.007378175514105413],
+      [0.01306580710473399],
+      [0.005438229413926055],
+      [0.01559207164907205],
+      [0.007497976053105356],
+      [0.01327795856827995],
+      [0.005526530758038588],
+      [0.02204519218088164],
+      [0.01060117775101382],
+      [0.01877333269084459],
+      [0.00781380661894053],
+      [0.02001283201397348],
+      [0.009623848489980729],
+      [0.0170426073132688],
+      [0.007093446860043523],
+      [0.01681485300040535],
+      [0.008085991904804354],
+      [0.0143192595888557],
+      [0.005959939409601683],
+      [0.01708787828271292],
+      [0.008217285364372072],
+      [0.0145517635478013],
+      [0.006056711836919557],
+      [0.02416007116849923],
+      [0.01161818898347029],
+      [0.02057432977490965],
+      [0.008563414755540757],
+      [0.01095174735555056],
+      [0.008072200842739543],
+      [0.01913496685581441],
+      [0.009201697278655068],
+      [0.01629503140027161],
+      [0.006782292004731834],
+      [0.009351106613197152],
+      [0.01655961626153459],
+      [0.006892417094094173],
+      [0.02749367841825353],
+      [0.0132212670023302],
+      [0.02341317633368553],
+      [0.009744994946783913]
+      ],
+     "Log Likelihood":-522.0390026738794,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *background*":        [
+[0.2130897909742414, 1]
+        ],
+       "non-synonymous/synonymous rate ratio for *test*":        [
+[0.05367176447095212, 1]
+        ]
+      },
+     "display order":1,
+     "estimated parameters":26
+    },
+   "Nucleotide GTR":{
+     "AIC-c":1130.795872905925,
+     "Equilibrium frequencies":      [
+[0.3347619047619048],
+      [0.2033333333333333],
+      [0.2466666666666667],
+      [0.2152380952380952]
+      ],
+     "Log Likelihood":-546.2152441452704,
+     "Rate Distributions":{
+       "Substitution rate from nucleotide A to nucleotide C":0.1157280802219541,
+       "Substitution rate from nucleotide A to nucleotide G":1,
+       "Substitution rate from nucleotide A to nucleotide T":0,
+       "Substitution rate from nucleotide C to nucleotide G":0.1604122535118794,
+       "Substitution rate from nucleotide C to nucleotide T":2.313607104947681,
+       "Substitution rate from nucleotide G to nucleotide T":0.1528462357734212
+      },
+     "display order":0,
+     "estimated parameters":19
+    }
+  },
+ "input":{
+   "file name":"/home/dcallan-adm/Documents/veg/CAPHEINE/work/6a/8adfdc16ef877c493cc257d23c98ea/pretend_DENV1_ref.part_NC_001477.1__capsid_protein_C__95-394_DENV1-nodups.fasta",
+   "number of sequences":7,
+   "number of sites":100,
+   "partition count":1,
+   "trees":{
+     "0":"(PP564823_1_2023_10_06,((PP563832_1_2023_08_28,PP563830_1_2023_09_02,PP563831_1_2023_08_29)Node3,(PP563839_1_2023_09_29,PP563838_1_2023_09_30)Node8)Node2,PP563845_1_2023_10_22)"
+    }
+  },
+ "model":{
+   "Q":    [
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+    ],
+   "alphabet":    [
+["AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT", "TAC", "TAT", "TCA", "TCC", "TCG", "TCT", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"]
+    ],
+   "ordering":{
+     "Factor I bipolar":0,
+     "Factor II secondary structure":1,
+     "Factor III volume":2,
+     "Factor IV composition":3,
+     "Factor V charge":4
+    },
+   "parameters":{
+     "lambda_Factor_III_volume":"Factor III volume",
+     "lambda_Factor_II_secondary_structure":"Factor II secondary structure",
+     "lambda_Factor_IV_composition":"Factor IV composition",
+     "lambda_Factor_I_bipolar":"Factor I bipolar",
+     "lambda_Factor_V_charge":"Factor V charge"
+    },
+   "residue_properties":{
+     "Factor I bipolar":{
+       "A":-0.6038471648233061,
+       "C":-1.372194149505415,
+       "D":1.072824912122625,
+       "E":1.38649848166705,
+       "F":-1.027868439614629,
+       "G":-0.3923473964334172,
+       "H":0.3433039718792401,
+       "I":-1.265933396304698,
+       "K":1.870802299139549,
+       "L":-1.041151033764719,
+       "M":-0.6774123016545719,
+       "N":0.9655424209103626,
+       "P":0.1931084841820725,
+       "Q":0.9512380887487276,
+       "R":1.571433061756759,
+       "S":-0.2329562666323415,
+       "T":-0.03269561636945143,
+       "V":-1.366063721436143,
+       "W":-0.6079341168694875,
+       "Y":0.2656518830017929
+      },
+     "Factor II secondary structure":{
+       "A":-1.330232386778897,
+       "C":0.475221663023938,
+       "D":0.3086744020630652,
+       "E":-1.48451849969357,
+       "F":-0.6027376027044098,
+       "G":1.688053557260477,
+       "H":-0.4259727183717044,
+       "I":-0.5588018222055293,
+       "K":-0.5731064949260951,
+       "L":-1.008377250566167,
+       "M":-1.557063625633582,
+       "N":0.8461213914214641,
+       "P":2.126389599912099,
+       "Q":-0.1827932821220867,
+       "R":-0.05609475231136144,
+       "S":1.42954768595311,
+       "T":0.3331966981554637,
+       "V":-0.2849695158404135,
+       "W":0.009298037268367709,
+       "Y":0.8481649160958307
+      },
+     "Factor III volume":{
+       "A":-0.3445293132340136,
+       "C":-0.4051709852318138,
+       "D":-1.718603788036881,
+       "E":0.6943706488988424,
+       "F":0.8889881078685267,
+       "G":0.6252673482501864,
+       "H":-0.7864143650009298,
+       "I":1.001809823213271,
+       "K":0.2506052352095138,
+       "L":-0.7074391642596085,
+       "M":1.043177785506344,
+       "N":0.6106945433514901,
+       "P":-0.7652602933737901,
+       "Q":-1.412574885164262,
+       "R":0.7061229109139199,
+       "S":-2.237583678622706,
+       "T":1.040357242622726,
+       "V":-0.2556822124000274,
+       "W":0.315947812013345,
+       "Y":1.455917227475868
+      },
+     "Factor IV composition":{
+       "A":1.630293655002852,
+       "C":-1.059000381337118,
+       "D":-0.2688255698874202,
+       "E":0.1174359673783979,
+       "F":-0.4121161401634496,
+       "G":1.08516648547448,
+       "H":-1.530405590795939,
+       "I":0.4081704577935299,
+       "K":-0.2875156442712501,
+       "L":1.314639065409281,
+       "M":-1.043425319350593,
+       "N":-0.1753751979682707,
+       "P":0.4372439068350431,
+       "Q":-0.5221799115348923,
+       "R":0.4569723186846413,
+       "S":0.6957899358113568,
+       "T":0.942914252664219,
+       "V":1.289718966230841,
+       "W":-2.209478293408426,
+       "Y":-0.8700229625672823
+      },
+     "Factor V charge":{
+       "A":-0.09353709405505788,
+       "C":-0.1633935055110449,
+       "D":-2.077715533208598,
+       "E":-0.5363882896154895,
+       "F":0.2640764618388941,
+       "G":1.322817670327799,
+       "H":-0.0499569474586623,
+       "I":0.5229938033821855,
+       "K":1.056209714679261,
+       "L":-0.5844546277732787,
+       "M":0.7767840688553127,
+       "N":0.5979772909083368,
+       "P":-0.8920791919831299,
+       "Q":-1.187526950526341,
+       "R":1.856674466133644,
+       "S":-1.696389250490137,
+       "T":0.8415134042411355,
+       "V":-0.8087642058429619,
+       "W":-0.1178907053883378,
+       "Y":0.9690494214864698
+      }
+    },
+   "translation-table":{
+     "AAA":"K",
+     "AAC":"N",
+     "AAG":"K",
+     "AAT":"N",
+     "ACA":"T",
+     "ACC":"T",
+     "ACG":"T",
+     "ACT":"T",
+     "AGA":"R",
+     "AGC":"S",
+     "AGG":"R",
+     "AGT":"S",
+     "ATA":"I",
+     "ATC":"I",
+     "ATG":"M",
+     "ATT":"I",
+     "CAA":"Q",
+     "CAC":"H",
+     "CAG":"Q",
+     "CAT":"H",
+     "CCA":"P",
+     "CCC":"P",
+     "CCG":"P",
+     "CCT":"P",
+     "CGA":"R",
+     "CGC":"R",
+     "CGG":"R",
+     "CGT":"R",
+     "CTA":"L",
+     "CTC":"L",
+     "CTG":"L",
+     "CTT":"L",
+     "GAA":"E",
+     "GAC":"D",
+     "GAG":"E",
+     "GAT":"D",
+     "GCA":"A",
+     "GCC":"A",
+     "GCG":"A",
+     "GCT":"A",
+     "GGA":"G",
+     "GGC":"G",
+     "GGG":"G",
+     "GGT":"G",
+     "GTA":"V",
+     "GTC":"V",
+     "GTG":"V",
+     "GTT":"V",
+     "TAA":"X",
+     "TAC":"Y",
+     "TAG":"X",
+     "TAT":"Y",
+     "TCA":"S",
+     "TCC":"S",
+     "TCG":"S",
+     "TCT":"S",
+     "TGA":"X",
+     "TGC":"C",
+     "TGG":"W",
+     "TGT":"C",
+     "TTA":"L",
+     "TTC":"F",
+     "TTG":"L",
+     "TTT":"F"
+    }
+  },
+ "runtime":"2.5.73",
+ "tested":{
+   "0":{
+     "Node2":"test",
+     "Node3":"test",
+     "Node8":"test",
+     "PP563830_1_2023_09_02":"background",
+     "PP563831_1_2023_08_29":"background",
+     "PP563832_1_2023_08_28":"background",
+     "PP563838_1_2023_09_30":"background",
+     "PP563839_1_2023_09_29":"background",
+     "PP563845_1_2023_10_22":"background",
+     "PP564823_1_2023_10_06":"background"
+    }
+  },
+ "timers":{
+   "Model fitting":{
+     "order":1,
+     "timer":0
+    },
+   "PRIME analysis":{
+     "order":2,
+     "timer":41
+    },
+   "Total time":{
+     "order":0,
+     "timer":43
+    }
+  }
+}