Performance Profile Index
For bin/pan_genome_post_analysis
  Run on Fri Mar 27 11:43:32 2015
Reported on Fri Mar 27 11:46:20 2015

Profile of bin/pan_genome_post_analysis for 58.3s (of 82.8s), executing 39877987 statements and 10165002 subroutine calls in 250 source files and 85 string evals.
Top 15 Subroutines
Calls P F Exclusive
Time
Inclusive
Time
Subroutine
39725314.11s4.11sBio::Roary::SplitGroups::::CORE:readline Bio::Roary::SplitGroups::CORE:readline (opcode)
72819323.63s5.15sBio::Roary::AnalyseGroups::::_count_num_files_in_group Bio::Roary::AnalyseGroups::_count_num_files_in_group
18216113.60s4.56sText::CSV_PP::::_combine Text::CSV_PP::_combine
10113.38s3.58sBio::Roary::Output::NumberOfGroups::::_single_iteration_gene_expansion Bio::Roary::Output::NumberOfGroups::_single_iteration_gene_expansion
2112.24s3.25sBio::Roary::Output::EmblGroups::::_build__groups_to_files Bio::Roary::Output::EmblGroups::_build__groups_to_files
1587215542.12s2.12sBio::Roary::AnalyseGroups::::_genes_to_file Bio::Roary::AnalyseGroups::_genes_to_file
18216112.06s2.06sIO::Handle::::CORE:print IO::Handle::CORE:print (opcode)
32985111.95s3.05sBio::Roary::AnnotateGroups::::_ids_grouped_by_gene_name_for_group Bio::Roary::AnnotateGroups::_ids_grouped_by_gene_name_for_group
18215111.73s8.87sBio::Roary::GroupStatistics::::_row Bio::Roary::GroupStatistics::_row
1111.05s1.52sBio::Roary::GroupStatistics::::_build__groups_to_files Bio::Roary::GroupStatistics::_build__groups_to_files
640518211.05s2.88sBio::Roary::AnnotateGroups::::_ids_to_gene_names Bio::Roary::AnnotateGroups::_ids_to_gene_names
1821511973ms1.38sBio::Roary::AnnotateGroups::::consensus_product_for_id_names Bio::Roary::AnnotateGroups::consensus_product_for_id_names
14926061959ms959msBio::Roary::AnalyseGroups::::CORE:readline Bio::Roary::AnalyseGroups::CORE:readline (opcode)
811877ms1.40sBio::Roary::ContigsToGeneIDsFromGFF::::_build_contig_to_idsBio::Roary::ContigsToGeneIDsFromGFF::_build_contig_to_ids
811855ms1.66sBio::Roary::GeneNamesFromGFF::::_build_ids_to_gene_name Bio::Roary::GeneNamesFromGFF::_build_ids_to_gene_name

You can view a treemap of subroutine exclusive time, grouped by package.
NYTProf also generates call-graph files in Graphviz format: inter-package calls, all inter-subroutine calls (probably too complex to render easily).

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Some table column headings can be clicked on to sort the table by that column.
Source Code Files — ordered by exclusive time then name
StmtsExclusive
Time
ReportsSource File
14028637.25sline • block • sublib/Bio/Roary/SplitGroups.pm
25729354.71sline • block • sublib/Bio/Roary/AnalyseGroups.pm
31403614.52sline • block • subText/CSV_PP.pm (including 1 string eval)
13295403.41sline • block • sublib/Bio/Roary/AnnotateGroups.pm
15207583.05sline • block • sublib/Bio/Roary/Output/EmblGroups.pm
28793642.76sline • block • subGraph.pm (including 1 string eval)
16329532.72sline • block • sublib/Bio/Roary/GroupStatistics.pm
72425702.43sline • block • sublib/Bio/Roary/Output/NumberOfGroups.pm
546732.15sline • block • subIO/Handle.pm (including 2 string evals)
7413311.51sline • block • sublib/Bio/Roary/ContigsToGeneIDsFromGFF.pm
5114231.47sline • block • sublib/Bio/Roary/GeneNamesFromGFF.pm
1018859876msline • block • subGraph/AdjacencyMap.pm
725291678msline • block • subGraph/Traversal.pm
838343620msline • block • subGraph/AdjacencyMap/Heavy.pm
467208613msline • block • sublib/Bio/Roary/OrderGenes.pm
887776573msline • block • subGraph/AdjacencyMap/Light.pm
6355msline • block • subbin/pan_genome_post_analysis
299398208msline • block • subHeap071/Fibonacci.pm
58695128msline • block • subClass/MOP/Class.pm
72886124msline • block • sublib/Bio/Roary/GroupLabels.pm
1200881811.5sline • block • subEval/Closure.pm (including 1 string eval)
9595.6msline • block • sublib/Bio/Roary/PostAnalysis.pm
4207190.1msline • block • sublib/Bio/Roary/InflateClusters.pm
3783589.4msline • block • subClass/MOP/Attribute.pm
3688682.4msline • block • subMoose/Meta/Attribute.pm
5972865.0msline • block • subGraph/Traversal/DFS.pm
2185059.5msline • block • subClass/MOP/Mixin/HasMethods.pm
2684658.6msline • block • subGraph/MSTHeapElem.pm
672439.9msline • block • subFile/Basename.pm
760439.0msline • block • subClass/MOP/Package.pm
11835.1msline • block • subB/Deparse.pm
3286534.6msline • block • subTry/Tiny.pm (including 1 string eval)
993531.5msline • block • subClass/MOP/Method/Accessor.pm
985931.1msline • block • subMoose/Meta/Class.pm
1470730.9msline • block • subClass/MOP/Instance.pm
1645428.2msline • block • sublib/Bio/Roary/ClustersRole.pm
1040022.9msline • block • subMoose/Meta/TypeConstraint.pm
983722.6msline • block • subSub/Exporter.pm
2003821.2msline • block • subHeap071/Elem.pm
330121.1msline • block • subutf8_heavy.pl
1021920.9msline • block • subClass/MOP/Mixin/AttributeCore.pm
534319.6msline • block • subClass/MOP.pm
763118.8msline • block • subMoose/Exporter.pm
550817.0msline • block • subClass/MOP/Mixin/HasAttributes.pm
524713.5msline • block • subSub/Install.pm
335312.9msline • block • subMoose/Util/TypeConstraints.pm
393812.5msline • block • subClass/MOP/Method/Wrapped.pm
459212.3msline • block • subClass/MOP/Method.pm
148811.9msline • block • subFile/Temp.pm
186911.5msline • block • subMoose.pm
291211.0msline • block • subModule/Runtime.pm
328610.8msline • block • subExporter.pm
50789.80msline • block • subClass/MOP/Method/Generated.pm
16049.70msline • block • subGetopt/Long.pm
24929.30msline • block • subMoose/Meta/Method/Accessor.pm
18028.29msline • block • subExporter/Heavy.pm
9077.29msline • block • subMoose/Util.pm
63296.84msline • block • subData/OptList.pm
22639.73msline • block • subbase.pm (including 36 string evals)
4976.35msline • block • subCarp.pm (including 1 string eval)
24316.10msline • block • subClass/MOP/Object.pm
39226.06msline • block • subClass/MOP/Class/Immutable/Trait.pm
3006.02msline • block • subDynaLoader.pm
44085.63msline • block • substrict.pm
10425.49msline • block • subClass/MOP/Method/Constructor.pm
1055.48msline • block • subBio/SeqUtils.pm
18075.36msline • block • subOpcode.pm
9435.19msline • block • subClass/MOP/Method/Meta.pm
8385.10msline • block • subMoose/Util/TypeConstraints/Builtins.pm
184.66msline • block • subBio/Tools/GFF.pm
424.49msline • block • subBio/Root/IO.pm
1704.61msline • block • subFile/Find/Rule.pm (including 27 string evals)
414.45msline • block • subData/Dumper.pm
394.03msline • block • subPOSIX.pm
2763.91msline • block • subMoose/Meta/Role.pm
103.90msline • block • subunicore/Heavy.pl
363.81msline • block • subFile/Find.pm
2063.79msline • block • subFile/Path.pm
493.63msline • block • subParams/Util.pm (including 2 string evals)
7403.61msline • block • subvars.pm
403.53msline • block • subSafe.pm (including 1 string eval)
83.43msline • block • subBio/PrimarySeq.pm
14913.34msline • block • subMoose/Meta/TypeConstraint/Registry.pm
5363.29msline • block • subparent.pm
7783.05msline • block • subconstant.pm
273.03msline • block • subStorable.pm
173.00msline • block • subBio/SeqFeature/Generic.pm
4482.97msline • block • subMoose/Meta/Method/Destructor.pm
512.90msline • block • subCwd.pm
72.77msline • block • subBio/PrimarySeqI.pm
3042.75msline • block • subBio/Tools/CodonTable.pm
392.74msline • block • subError.pm
562.72msline • block • subB.pm
4462.58msline • block • subClass/MOP/Method/Inlined.pm
132.52msline • block • subBio/RangeI.pm
10612.50msline • block • subwarnings.pm
82.47msline • block • subBio/Tools/GuessSeqFormat.pm
162.45msline • block • subBio/LocatableSeq.pm
312.40msline • block • subFile/Copy.pm (including 1 string eval)
1212.29msline • block • sublib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm
252.26msline • block • subClass/Load.pm
792.21msline • block • subFile/Spec/Unix.pm
4432.05msline • block • subMoose/Meta/TypeConstraint/Class.pm
111.95msline • block • subBio/Annotation/Collection.pm
171.94msline • block • subBio/SeqIO.pm
171.93msline • block • subBio/SeqFeatureI.pm
91.84msline • block • subBio/Location/Fuzzy.pm
61.79msline • block • subBio/Location/Split.pm
401.95msline • block • subBio/Root/Root.pm (including 2 string evals)
191.74msline • block • subBio/Root/RootI.pm
201.69msline • block • subMoose/Meta/Role/Application/RoleSummation.pm
861.67msline • block • subModule/Implementation.pm
151.67msline • block • subBio/Tools/IUPAC.pm
1881.65msline • block • subMoose/Meta/Method/Constructor.pm
3381.65msline • block • suboverload.pm
2431.63msline • block • subMoose/Meta/Role/Application/ToClass.pm
81.62msline • block • subBio/Location/Atomic.pm
141.54msline • block • subScalar/Util.pm (including 1 string eval)
281.53msline • block • subClass/MOP/Mixin/HasOverloads.pm
71.51msline • block • subGraph/TransitiveClosure/Matrix.pm
601.46msline • block • subException/Class/Base.pm
1021.43msline • block • subPackage/DeprecationManager.pm
251.42msline • block • subMRO/Compat.pm
241.42msline • block • sublib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
121.41msline • block • subBio/Seq.pm
3251.39msline • block • subClass/MOP/MiniTrait.pm
581.39msline • block • subSub/Exporter/Progressive.pm
391.38msline • block • subre.pm
2011.36msline • block • subMoose/Role.pm
151.35msline • block • subMoose/Util/MetaRole.pm
511.35msline • block • subAutoLoader.pm
1041.48msline • block • subText/CSV.pm (including 2 string evals)
301.30msline • block • subClass/MOP/Overload.pm
381.28msline • block • subPackage/Stash.pm
191.26msline • block • subDevel/StackTrace.pm
1961.26msline • block • subMoose/Meta/Role/Attribute.pm
271.20msline • block • subMoose/Object.pm
161.20msline • block • subMoose/Meta/TypeConstraint/Union.pm
901.27msline • block • subException/Class.pm (including 2 string evals)
1301.16msline • block • subMoose/Meta/Role/Application.pm
611.16msline • block • subConfig.pm
191.16msline • block • subMoose/Meta/Role/Composite.pm
1121.15msline • block • subMoose/Meta/TypeConstraint/Parameterized.pm
131.14msline • block • subBio/Root/Exception.pm
151.14msline • block • subBio/Factory/FTLocationFactory.pm
661.11msline • block • subList/Util.pm (including 1 string eval)
701.08msline • block • subGraph/Attribute.pm
101.01msline • block • subGraph/AdjacencyMap/Vertex.pm
7967µsline • block • subBio/DB/InMemoryCache.pm
231955µsline • block • submetaclass.pm
7948µsline • block • subBio/Seq/SeqBuilder.pm
128943µsline • block • subClass/MOP/Mixin.pm
7936µsline • block • subBio/Location/Simple.pm
16926µsline • block • subFile/Grep.pm
21925µsline • block • subDevel/OverloadInfo.pm
11911µsline • block • subGraph/AdjacencyMatrix.pm
3892µsline • block • subGraph/BitMatrix.pm
38862µsline • block • subFindBin.pm
90820µsline • block • subMoose/Meta/TypeConstraint/Parameterizable.pm
235802µsline • block • subErrno.pm (including 1 string eval)
28788µsline • block • subList/MoreUtils.pm
11782µsline • block • subBio/Range.pm
20774µsline • block • subSub/Identify.pm
17753µsline • block • subMoose/Meta/TypeCoercion.pm
12740µsline • block • subMoose/Meta/Role/Application/ToRole.pm
21739µsline • block • sublib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm
38730µsline • block • subClass/MOP/Module.pm
23729µsline • block • subMoose/Meta/TypeConstraint/DuckType.pm
60706µsline • block • subMoose/Meta/TypeConstraint/Role.pm
7702µsline • block • subTie/Hash.pm
14686µsline • block • subPackage/Stash/XS.pm
12681µsline • block • subFcntl.pm
7674µsline • block • subBio/LocationI.pm
10652µsline • block • subSymbol.pm
33638µsline • block • subDevel/StackTrace/Frame.pm
20629µsline • block • subMoose/Meta/TypeConstraint/Enum.pm
13624µsline • block • subClass/Load/XS.pm
57594µsline • block • sublib/Bio/Roary/ParseGFFAnnotationRole.pm
11587µsline • block • subIO.pm
79546µsline • block • subGraph/Undirected.pm
12534µsline • block • subMoose/Meta/Method/Delegation.pm
14526µsline • block • subMoose/Meta/Class/Immutable/Trait.pm
15514µsline • block • sublib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm
13510µsline • block • subDevel/GlobalDestruction.pm (including 1 string eval)
7504µsline • block • subGraph/TransitiveClosure.pm
14490µsline • block • subText/Glob.pm
3484µsline • block • subGraph/UnionFind.pm
18479µsline • block • suboverloading.pm
18478µsline • block • subIO/Seekable.pm (including 1 string eval)
10458µsline • block • subMoose/Meta/Method/Augmented.pm
7450µsline • block • subBio/Annotation/SimpleValue.pm
10450µsline • block • subMoose/Meta/Method/Overridden.pm
8449µsline • block • submro.pm
8408µsline • block • sublib/Bio/Roary/CommandLine/Common.pm
9404µsline • block • subMoose/Deprecated.pm
7402µsline • block • subBio/FeatureHolderI.pm
18401µsline • block • subMoose/Meta/Role/Application/ToInstance.pm
21388µsline • block • subMoose/Meta/Mixin/AttributeCore.pm
10375µsline • block • subGraph/SPTHeapElem.pm
15371µsline • block • subSub/Name.pm
50336µsline • block • subMoose/Meta/Method/Meta.pm
11333µsline • block • subFile/Spec.pm
5329µsline • block • subBio/IdentifiableI.pm
38305µsline • block • subMoose/Meta/Attribute/Native.pm
5304µsline • block • subBio/Annotation/TypeManager.pm
14301µsline • block • subMoose/Meta/TypeCoercion/Union.pm
3278µsline • block • subGraph/Matrix.pm
8275µsline • block • subArray/Utils.pm
11269µsline • block • subMoose/Meta/Role/Method/Conflicting.pm
15265µsline • block • subClone.pm
48260µsline • block • subClass/Data/Inheritable.pm
8252µsline • block • subNumber/Compare.pm
5252µsline • block • subBio/Seq/SeqFactory.pm
13249µsline • block • subMoose/Meta/Role/Method/Required.pm
7219µsline • block • subSelectSaver.pm
4213µsline • block • subMoose/Meta/Object/Trait.pm
5203µsline • block • subBio/SeqI.pm
5198µsline • block • subBio/Factory/SequenceStreamI.pm
11189µsline • block • subMoose/Meta/Instance.pm
7188µsline • block • subBio/Location/SplitLocationI.pm
5183µsline • block • subutf8.pm
8182µsline • block • subBio/Location/WidestCoordPolicy.pm
9176µsline • block • sublib/Bio/Roary/JobRunner/Role.pm
7171µsline • block • subBio/Factory/ObjectBuilderI.pm
5166µsline • block • subBio/AnnotationCollectionI.pm
5162µsline • block • subBio/Location/FuzzyLocationI.pm
7162µsline • block • subBio/DB/RandomAccessI.pm
8151µsline • block • subMoose/Meta/Role/Method.pm
5151µsline • block • subBio/DescribableI.pm
5150µsline • block • subBio/DB/SeqI.pm
5142µsline • block • subBio/AnnotationI.pm
21136µsline • block • subsubs.pm
7131µsline • block • subBio/Factory/ObjectFactoryI.pm
3129µsline • block • sublib/Bio/Roary/Exceptions.pm
8128µsline • block • subClass/MOP/Deprecated.pm
11124µsline • block • subMoose/Meta/Method.pm
5124µsline • block • subBio/Location/CoordinatePolicyI.pm
5123µsline • block • subunicore/To/Cf.pl
7118µsline • block • subBio/Factory/LocationFactoryI.pm
7113µsline • block • subBio/SeqAnalysisParserI.pm
2897µsline • block • subwarnings/register.pm
687µsline • block • subCarp/Heavy.pm
2472µsline • block • subif.pm
572µsline • block • subBio/AnnotatableI.pm
560µsline • block • subBio/Factory/SequenceFactoryI.pm
1359µsline • block • subfeature.pm
532µsline • block • subbytes.pm
514µsline • block • subinteger.pm
15µsline • block • subunicore/lib/Perl/_PerlIDS.pl
00sline • block • subXSLoader.pm
3987805653.1sTotal (-69 statements are unaccounted for)
159512212msAverage
1.41msMedian
0.00121Deviation