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chapmanb/svCandidateGenerationStats.tsv

Created April 27, 2018 13:57
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huD57BBF manta runtime stats
Raw
svCandidateGenerationStats.tsv
We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 1 column, instead of 2. in line 1.
EdgeStatsReport
SVGenTotalHours 59.1786h wall, 0.5012h user + 0.0591h system = 0.5603h CPU (0.95%)
NonEdgeHours 0.0197h wall, 0.0115h user + 0.0038h system = 0.0152h CPU (77.53%)
[AllEdges]
InputEdgeCount 101415
InputEdgeCandidatesPerEdge:
0 52679
1 43118
2 5233
3 296
4 49
5+ 40
CandidateCount 54946
ComplexCandidateCount 7401
EdgeFilter 49223
SemiMappedFilter 886
ComplexLowCountFilter 4017
ComplexLowSignalFilter 0
UnmatchedReadPairFilter 0
SpanningComplexCandidateFiltered 33892
JunctionAssemblyOverlapSkipped 0
JunctionCount 20984
ComplexJunctionCount 7401
BreaksPerJunction:
0 0
1 20562
2 211
3+ 0
TotalAssemblyCandidates 5593
TotalSpanningAssemblyCandidates 4259
AssemblyCandidatesPerJunction:
0 15393
1 5586
2 2
3 1
4 0
5+ 0
totalHours 59.1590h wall, 0.4897h user + 0.0553h system = 0.5450h CPU (0.92%)
totalSecsPerEdge 2.1000s wall, 0.0174s user + 0.0020s system = 0.0193s CPU (0.92%)
totalSecsPerCand 3.8760s wall, 0.0321s user + 0.0036s system = 0.0357s CPU (0.92%)
candiHours 56.2706h wall, 0.1677h user + 0.0258h system = 0.1936h CPU (0.34%)
candiSecsPerEdge 1.9975s wall, 0.0060s user + 0.0009s system = 0.0069s CPU (0.34%)
candiSecsPerCand 3.6868s wall, 0.0110s user + 0.0017s system = 0.0127s CPU (0.34%)
assemHours 2.4747h wall, 0.2274h user + 0.0197h system = 0.2471h CPU (9.98%)
assemSecsPerEdge 0.0878s wall, 0.0081s user + 0.0007s system = 0.0088s CPU (9.98%)
assemSecsPerCand 0.1621s wall, 0.0149s user + 0.0013s system = 0.0162s CPU (9.98%)
scoreHours 0.4129h wall, 0.0939h user + 0.0097h system = 0.1036h CPU (25.10%)
scoreSecsPerEdge 0.0147s wall, 0.0033s user + 0.0003s system = 0.0037s CPU (25.10%)
scoreSecsPerCand 0.0271s wall, 0.0062s user + 0.0006s system = 0.0068s CPU (25.10%)
nocatHours 0.0007h wall, 0.0006h user + 0.0001h system = 0.0007h CPU (96.35%)
nocatSecsPerEdge 0.0000s wall, 0.0000s user + 0.0000s system = 0.0000s CPU (96.35%)
nocatSecsPerCand 0.0000s wall, 0.0000s user + 0.0000s system = 0.0000s CPU (96.35%)
[RemoteEdges]
InputEdgeCount 61395
InputEdgeCandidatesPerEdge:
0 49269
1 11506
2 538
3 65
4 14
5+ 3
CandidateCount 12850
ComplexCandidateCount 626
EdgeFilter 49223
SemiMappedFilter 655
ComplexLowCountFilter 6
ComplexLowSignalFilter 0
UnmatchedReadPairFilter 0
SpanningComplexCandidateFiltered 1011
JunctionAssemblyOverlapSkipped 0
JunctionCount 11791
ComplexJunctionCount 626
BreaksPerJunction:
0 0
1 11383
2 204
3+ 0
TotalAssemblyCandidates 4956
TotalSpanningAssemblyCandidates 3664
AssemblyCandidatesPerJunction:
0 6838
1 4949
2 2
3 1
4 0
5+ 0
totalHours 19.6012h wall, 0.3188h user + 0.0329h system = 0.3518h CPU (1.79%)
totalSecsPerEdge 1.1494s wall, 0.0187s user + 0.0019s system = 0.0206s CPU (1.79%)
totalSecsPerCand 5.4914s wall, 0.0893s user + 0.0092s system = 0.0985s CPU (1.79%)
candiHours 18.6717h wall, 0.0787h user + 0.0108h system = 0.0895h CPU (0.48%)
candiSecsPerEdge 1.0948s wall, 0.0046s user + 0.0006s system = 0.0052s CPU (0.48%)
candiSecsPerCand 5.2310s wall, 0.0220s user + 0.0030s system = 0.0251s CPU (0.48%)
assemHours 0.5228h wall, 0.1477h user + 0.0125h system = 0.1602h CPU (30.65%)
assemSecsPerEdge 0.0307s wall, 0.0087s user + 0.0007s system = 0.0094s CPU (30.65%)
assemSecsPerCand 0.1465s wall, 0.0414s user + 0.0035s system = 0.0449s CPU (30.65%)
scoreHours 0.4062h wall, 0.0921h user + 0.0095h system = 0.1016h CPU (25.01%)
scoreSecsPerEdge 0.0238s wall, 0.0054s user + 0.0006s system = 0.0060s CPU (25.01%)
scoreSecsPerCand 0.1138s wall, 0.0258s user + 0.0027s system = 0.0285s CPU (25.01%)
nocatHours 0.0004h wall, 0.0003h user + 0.0001h system = 0.0004h CPU (97.91%)
nocatSecsPerEdge 0.0000s wall, 0.0000s user + 0.0000s system = 0.0000s CPU (97.91%)
nocatSecsPerCand 0.0001s wall, 0.0001s user + 0.0000s system = 0.0001s CPU (97.91%)
[SelfEdges]
InputEdgeCount 40020
InputEdgeCandidatesPerEdge:
0 3410
1 31612
2 4695
3 231
4 35
5+ 37
CandidateCount 42096
ComplexCandidateCount 6775
EdgeFilter 0
SemiMappedFilter 231
ComplexLowCountFilter 4011
ComplexLowSignalFilter 0
UnmatchedReadPairFilter 0
SpanningComplexCandidateFiltered 32881
JunctionAssemblyOverlapSkipped 0
JunctionCount 9193
ComplexJunctionCount 6775
BreaksPerJunction:
0 0
1 9179
2 7
3+ 0
TotalAssemblyCandidates 637
TotalSpanningAssemblyCandidates 595
AssemblyCandidatesPerJunction:
0 8555
1 637
2 0
3 0
4 0
5+ 0
totalHours 39.5578h wall, 0.1709h user + 0.0224h system = 0.1933h CPU (0.49%)
totalSecsPerEdge 3.5584s wall, 0.0154s user + 0.0020s system = 0.0174s CPU (0.49%)
totalSecsPerCand 3.3829s wall, 0.0146s user + 0.0019s system = 0.0165s CPU (0.49%)
candiHours 37.5988h wall, 0.0891h user + 0.0150h system = 0.1041h CPU (0.28%)
candiSecsPerEdge 3.3822s wall, 0.0080s user + 0.0014s system = 0.0094s CPU (0.28%)
candiSecsPerCand 3.2154s wall, 0.0076s user + 0.0013s system = 0.0089s CPU (0.28%)
assemHours 1.9519h wall, 0.0797h user + 0.0072h system = 0.0869h CPU (4.45%)
assemSecsPerEdge 0.1756s wall, 0.0072s user + 0.0006s system = 0.0078s CPU (4.45%)
assemSecsPerCand 0.1669s wall, 0.0068s user + 0.0006s system = 0.0074s CPU (4.45%)
scoreHours 0.0067h wall, 0.0019h user + 0.0002h system = 0.0020h CPU (30.44%)
scoreSecsPerEdge 0.0006s wall, 0.0002s user + 0.0000s system = 0.0002s CPU (30.44%)
scoreSecsPerCand 0.0006s wall, 0.0002s user + 0.0000s system = 0.0002s CPU (30.44%)
nocatHours 0.0003h wall, 0.0003h user + 0.0000h system = 0.0003h CPU (94.39%)
nocatSecsPerEdge 0.0000s wall, 0.0000s user + 0.0000s system = 0.0000s CPU (94.39%)
nocatSecsPerCand 0.0000s wall, 0.0000s user + 0.0000s system = 0.0000s CPU (94.39%)
Raw
svLocusGraphStats.tsv
We can make this file beautiful and searchable if this error is corrected: It looks like row 13 should actually have 2 columns, instead of 1. in line 12.
GraphBuildTime 336.5822h wall, 0.5883h user + 0.0517h system = 0.6400h CPU (0.19%)
GraphMergeTime 0.0008h wall, 0.0007h user + 0.0000h system = 0.0008h CPU (97.19%)
disjointSubgraphs 72528
nodes 132258
directedEdges 163151
selfEdges 40051
totalGraphEvidence 2242045
totalCleaned 9616330
highestSearchCount 392
isMaxSearchCount 0
highestSearchDensity 0.311538
isMaxSearchDensity 0
[Sample0]
Source /keep/61366c55634ae58f339efe66caecefd6+48334/huD57BBF-sort.bam
MinMapqFiltered 29536625 0.0468
NotFiltered 601486818 0.9532
NotFilteredAndIgnored 597045747 0.9462
NotFilteredAndAnomalousPair 3074536 0.0049
NotFilteredAndAnomalousPairRemotes 2545499 0.0040
NotFilteredAndSplitRead 1590194 0.0025
NotFilteredAndSplitReadInAnomalousPair 223659 0.0004
NotFilteredAndSplitReadSupplementarySegments 673990 N/A
NotFilteredAndLargeIndel 0 0.0000
NotFilteredAndSemiAligned 0 0.0000
EvidenceType_pair 0 0.0000
EvidenceType_local_pair 2743216 0.6869
EvidenceType_cigar 0 0.0000
EvidenceType_softclip 0 0.0000
EvidenceType_semialign 0 0.0000
EvidenceType_shadow 0 0.0000
EvidenceType_split_align 1250153 0.3131
EvidenceType_unknown 0 0.0000
ClosePairs 58268
NodeRegionSizequantile:
0.25 64
0.5 275
0.75 382
0.9 531
0.95 607
0.99 884
NodeEdgeCount:
0 0
1 122254
2 6286
3 1698
4 773
5 471
6 279
7 171
8 106
9+ 220
NodeObservationCount:
0 32024
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 31535
10 18
11 19
12 28773
13 24
14 34
15 6930
16 18
17 12
18 6495
19 15
20 18
21 3323
22 22
23 9
24 3034
25 10
26 18
27 2099
28 19
29+ 17809
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