findShmTrees report
MiXCR generates a comprehensive summary of search for trees process. Find trees reports may be generated right along with findShmTrees command using -r/--report for txt report and -j/--json-report for report in a json format, or can be exported using exportReports command.
Show sample report
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Analysis date: Thu Oct 06 17:42:26 CEST 2022
Input file(s): alleles/MRK_p02_Bmem_1_CGTACTAG-AAGGAGTA_L00M.with_alleles.clns,alleles/MRK_p03_Bmem_1_TCCTGAGC-GTAAGGAG_L00M.with_alleles.clns
Output file(s): trees/result.shmt
Version: ; built=Thu Oct 06 17:39:13 CEST 2022; rev=585abb5a1a; lib=repseqio.v2.0
Command line arguments: findShmTrees -j trees/report.json -r trees/report.txt alleles/MRK_p02_Bmem_1_CGTACTAG-AAGGAGTA_L00M.with_alleles.clns alleles/MRK_p03_Bmem_1_TCCTGAGC-GTAAGGAG_L00M.with_alleles.clns trees/result.shmt
Analysis time: 2.58s
Step 1: Building initial trees
Clones was added: 254
Trees created: 101
Step 2: Attaching clones by distance change
Clones was added: 6
Step 3: Combining trees
Trees combined: 0
Total trees count: 101
Total clones count in trees: 260
======================================
{
"type": "buildSHMTreeReport",
"commandLine": "findShmTrees -j trees/report.json -r trees/report.txt alleles/MRK_p02_Bmem_1_CGTACTAG-AAGGAGTA_L00M.with_alleles.clns alleles/MRK_p03_Bmem_1_TCCTGAGC-GTAAGGAG_L00M.with_alleles.clns trees/result.shmt",
"inputFiles": [
"alleles/MRK_p02_Bmem_1_CGTACTAG-AAGGAGTA_L00M.with_alleles.clns",
"alleles/MRK_p03_Bmem_1_TCCTGAGC-GTAAGGAG_L00M.with_alleles.clns"
],
"outputFiles": [
"trees/result.shmt"
],
"version": "; built=Thu Oct 06 17:39:13 CEST 2022; rev=585abb5a1a; lib=repseqio.v2.0",
"stepResults": [
{
"step": {
"name": "BuildingInitialTrees",
"algorithm": {
"type": "BronKerbosch",
"commonMutationsCountForClustering": 5,
"maxNDNDistanceForClustering": 1.0
}
},
"clonesWasAdded": 254,
"cloneNodesWasAdded": 253,
"treesCountDelta": 101,
"commonVJMutationsCounts": {
"size": 101,
"sum": "..."
},
"clonesCountInTrees": {
"size": 101,
"sum": "..."
},
"wildcardsScore": {
"size": 101,
"sum": "..."
},
"wildcardsScoreForRoots": {
"size": 101,
"sum": "..."
},
"maxNDNsWildcardsScoreInTree": {
"size": 101,
"sum": "..."
},
"surenessOfDecisions": {
"size": 101,
"sum": "..."
}
},
{
"step": {
"name": "AttachClonesByDistanceChange",
"threshold": 0.45,
"maxNDNDistance": 1.5
},
"clonesWasAdded": 6,
"cloneNodesWasAdded": 6,
"treesCountDelta": 0,
"commonVJMutationsCounts": {
"size": 101,
"sum": "..."
},
"clonesCountInTrees": {
"size": 101,
"sum": "..."
},
"wildcardsScore": {
"size": 101,
"sum": "..."
},
"wildcardsScoreForRoots": {
"size": 101,
"sum": "..."
},
"maxNDNsWildcardsScoreInTree": {
"size": 101,
"sum": "..."
},
"surenessOfDecisions": {
"size": 101,
"sum": "..."
}
},
{
"step": {
"name": "CombineTrees",
"maxNDNDistanceBetweenRoots": 0.3
},
"clonesWasAdded": 0,
"cloneNodesWasAdded": 0,
"treesCountDelta": 0,
"commonVJMutationsCounts": {
"size": 101,
"sum": "..."
},
"clonesCountInTrees": {
"size": 101,
"sum": "..."
},
"wildcardsScore": {
"size": 101,
"sum": "..."
},
"wildcardsScoreForRoots": {
"size": 101,
"sum": "..."
},
"maxNDNsWildcardsScoreInTree": {
"size": 101,
"sum": "..."
},
"surenessOfDecisions": {
"size": 101,
"sum": "..."
}
}
]
}
Step N: ...- Summary of step result.
Clones was added:- how many clones was added to any tree,Trees created:- how many trees was created on this step,Trees combined:- how many trees was combined. Total trees count- Total count of trees found by command.
Total clones count in trees- How many uniq clones included in found trees.
stepResults- Stats for every step.
step- name and parameters of step,clonesWasAdded- count of uniq clones that was added,cloneNodesWasAdded- count of clones that are uniq by target sequence (tree structure doesn't distinct C genes and sample names, that clones will be on the same node),treesCountDelta- change of tree count,commonVJMutationsCounts- stats of VJ mutations count of MRCA,clonesCountInTrees- stats of clones count,wildcardsScore- stats of wildcards in NDN (average for every tree),wildcardsScoreForRoots- stats of wildcards in NDN (for MRCA nodes),maxNDNsWildcardsScoreInTree- stats of wildcards in NDN (max for every tree),surenessOfDecisions- stats of main metric that used on this step