Problem running Beast - Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

[Jose Manuel Latorre Estivalis]

Hello,
I have an alignment of 400 amino acid sequences that I am trying to classify within a superfamily (different types of kinases).
My sequences have very different length, between 137 and 5000 residues.
I have tried to run Beast with different xml file inputs created by Beauti. I have tried different MCMC values, from 10.000 to 30 M. Beast works fine if I use few sequences (10).
I have tried to run Beast in my PC and Cipres Science Gateway, obtaining the same results. I load the alignment and the program starts, however, it runs until this step:

Random number seed: 1499364072986


Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser
line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser



Loading additional development parsers from development_parsers.properties, which is additional set of parsers only available for development version ...

WARNING: parser - dr.app.beagle.multidimensionalscaling.MultiDimensionalScalingLikelihood in development_parsers.properties is duplicated, which is REPLACING the same parser loaded previously.

Parsing XML file: Rho-Dmel-align.xml
  File encoding: UTF8
Looking for plugins in /home/jose/Programas/BEASTv1.8.2/lib/plugins
Read alignment: alignment
  Sequences = 438
      Sites = 19965
   Datatype = amino acid
Site patterns 'patterns' created from positions 1-19965 of alignment 'alignment'
  unique pattern count = 13777
Using Yule prior on tree
Creating the tree model, 'treeModel'

SEQUENCES
-
-
-
-

 tree height = 291.96462772192564
Using strict molecular clock model.
Creating site model.
  4 category discrete gamma with initial shape = 0.5
Using Java AminoAcid likelihood core java.lang.UnsatisfiedLinkError: no AminoAcidLikelihoodCore in java.library.path
Looking for AminoAcidLikelihoodCore in /usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
TreeLikelihood(treeModel) using Java amino acid likelihood core
  Ignoring ambiguities in tree likelihood.
  With 13777 unique site patterns.
Branch rate model used: strictClockBranchRates
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at dr.evomodel.treelikelihood.AbstractLikelihoodCore.createNodePartials(Unknown Source)
    at dr.evomodel.treelikelihood.TreeLikelihood.<init>(Unknown Source)
    at dr.evomodelxml.treelikelihood.TreeLikelihoodParser.parseXMLObject(Unknown Source)
    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.convert(Unknown Source)
    at dr.xml.XMLParser.parse(Unknown Source)
    at dr.app.beast.BeastMain.<init>(Unknown Source)
    at dr.app.beast.BeastMain.main(Unknown Source)

Thanks a lot for your help
Jose

[Andrew Rambaut]

Hi Jose,

I suggest you try using the BEAGLE library using the -beagle command line option. Here you are using the java implementation of the likelihood calculator which means all your data will be loaded into the Java heap. It will also be much slower than using BEAGLE. 

Best,

Andrew

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[Jose Manuel Latorre Estivalis]

Dear Andrew,
Thanks a lot for your answer,

I have tried to perform the analysis in BEAST v1.8.4, 2002-2016 program available at Cipres Science Gateway without using Beagle.
 However, it appeared the following message and the job did not finished:

CIPRES_THREADSPP=1
CIPRES_NP=1
running:
beast -threads 1 -beagle_off infile.xml

                  BEAST v1.8.4, 2002-2016
       Bayesian Evolutionary Analysis Sampling Trees
                 Designed and developed by
   Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard
                             
               Department of Computer Science
                   University of Auckland
                  ale...@cs.auckland.ac.nz
                             
             Institute of Evolutionary Biology
                  University of Edinburgh
                     a.ra...@ed.ac.uk
                             
              David Geffen School of Medicine
           University of California, Los Angeles
                     msuc...@ucla.edu
                             
                Downloads, Help & Resources:
                     http://beast.bio.ed.ac.uk
                             
Source code distributed under the GNU Lesser General Public License:
              http://github.com/beast-dev/beast-mcmc
                             
                     BEAST developers:
    Alex Alekseyenko, Guy Baele, Trevor Bedford, Filip Bielejec, Erik Bloomquist, Matthew Hall,
    Joseph Heled, Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
    Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
              Oliver Pybus, Chieh-Hsi Wu, Walter Xie
                             
                         Thanks to:
        Roald Forsberg, Beth Shapiro and Korbinian Strimmer


Random number seed: 1499787270476


Parsing XML file: infile.xml
  File encoding: ISO8859_15
Looking for plugins in /projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-BEAST_TG-2C3A77CA30C54DE185EA7300D1351812/plugins

Read alignment: alignment
  Sequences = 438
      Sites = 19965
   Datatype = amino acid
Site patterns 'patterns' created from positions 1-19965 of alignment 'alignment'
  unique pattern count = 13777
Using Yule prior on tree
Creating the tree model, 'treeModel'

  initial tree topology = ((((((((((((((((((((((CG4523DmelOther_NKF2,pllDmelTKL_IRAK),(RPRC001790,RPRC004857)),RPRC005609),(CG14217DmelSTE_STE20_TAO,RPRC009486)),(RPRC015112,mnbDmelCMGC_DYRK_DYRK1)),(((Cdk5DmelCMGC_CDK_CDK5,tkvDmelTKL_STKR_Type1),(RPRC003040,RPRC004230)),CG8485DmelCAMK_CAMKL_SNRK)),(RPRC004208,RPRC004552)),RPRC012957),(((((RPRC001869,gekDmelAGC_DMPK_GEK),RPRC007591),CkIalphaDmelCK1_CK1_CK1-A),((RPRC007079,rokDmelAGC_DMPK_ROCK),CG8173DmelOther_TOPK)),(CG10738DmelRGC_RGC,CG1951DmelOther_SCY1))),RPRC011597),(((((((Pk61CDmelAGC_PDK1,drlDmelTK_Ryk),Src42ADmelTK_Src_Frk),RPRC001740),(((RPRC009624,smi35ADmelCMGC_DYRK_DYRK2),sggDmelCMGC_GSK),(AblDmelTK_Abl,Par-1DmelCAMK_CAMKL_MARK))),(((CG6498DmelAGC_MAST_MAST,wtsDmelAGC_NDR),CG1344DmelOther_SCY1),((CG6535DmelAtypical_PIKK_ATM,hopDmelTK_Jak),(Gprk2DmelAGC_GRK_GRK,RPRC005800)))),CG9962DmelCK1_CK1_CK1-Unclassified),((((CG6114DmelCAMK_CAMKL_BRSK,RPRC010540),RPRC000333),(CG4041DmelOther_TBCK,hepDmelSTE_STE7_MEK7)),((dcoDmelCK1_CK1_CK1-D,poloDmelOther_PLK_PLK1),RPRC002851)))),((((EgfrDmelTK_EGFR,RPRC005685),CG8789DmelTKL_MLK_LZK),(AlkDmelTK_ALK,aurDmelOther_Aur)),(RPRC008734,ninaCDmelSTE_STE20_NinaC))),RPRC001078),(Takl2DmelTKL_MLK_TAK1,btlDmelTK_FGFR)),(((((((((((((RPRC000167,RPRC001641),RPRC015063),CG7156DmelAGC_RSKL),Gprk1DmelAGC_GRK_BARK),(HaspinDmelOther_Haspin,RPRC002914)),(CG11228DmelSTE_STE20_MST,putDmelTKL_STKR_Type2)),(((JIL1DmelAGC_RSK_MSK,msnDmelSTE_STE20_MSN),lokDmelCAMK_RAD53),DoaDmelCMGC_CLK)),((((RPRC007732,mei-41DmelAtypical_PIKK_ATR),CG7597DmelCMGC_CDK_CRK7),PR2DmelTK_Ack),((CG2577DmelCK1_CK1_CK1-Unclassified,aPKCDmelAGC_PKC_Iota),(RPRC005688,RPRC009634)))),(RPRC012309,Src64BDmelTK_Src_Src-Unclassified)),((Cad96CaDmelTK_TK-Unique,RPRC001666),RPRC007812)),((((((((RPRC004775,RPRC006548),RPRC013140),Tak1DmelTKL_MLK_TAK1),(RPRC012489,gishDmelCK1_CK1_CK1-G)),RPRC015071),CG6800DmelCMGC_CDK_CDK-Unclassified),((AckDmelTK_Ack,CG4290DmelCAMK_CAMKL_QIK),(RPRC010391,SNF1ADmelCAMK_CAMKL_AMPK))),CkIIalphaDmelCMGC_CK2)),((((CG4629DmelCAMK_CAMKL_NIM1,RPRC006894),CG8726DmelOther_Slob),NakDmelOther_NAK_BIKE),ksrDmelTKL_RAF_KSR)),((((CG7643DmelOther_TTK,PKCdeltaDmelAGC_PKC_Delta),CG14163DmelOther_SCY1),CG17698DmelOther_CAMKK_Meta),(((Cdk8DmelCMGC_CDK_CDK8,RPRC012077),weeDmelOther_WEE),CG12147DmelCK1_CK1_CK1-Unclassified)))),((((((((((((RPRC001637-5-RPRC005426-7,RPRC013601),RPRC007843),RPRC013126),((RPRC000321,RPRC013655),RPRC009035-33-RPRC008857)),((((auxillinDmelOther_NAK_GAK,pngDmelOther_Other-Unique),RPRC003670),Nek2DmelOther_NEK_NEK2),Myt1DmelOther_WEE)),(((CG9746DmelOther_VPS15,RPRC005429-),RPRC012179),ik2DmelOther_IKK)),(RPRC000863-4,RPRC009810)),(((CG4527DmelSTE_STE20_SLK,btDmelCAMK_MLCK),Fak56DDmelTK_FAK),RPRC006659)),(((RPRC006429,tlkDmelOther_TLK),(TieDmelTK_TK-Unique,bskDmelCMGC_MAPK_JNK)),CG12069DmelAGC_PKA)),((Dsor1DmelSTE_STE7_MEK1,RPRC014583-92),S6kIIDmelAGC_RSK_p70)),(Akt1DmelAGC_Akt,CG3105DmelCAMK_CAMKL_PASK)),(((((((((CG9222DmelCAMK_TSSK,phlDmelTKL_RAF_RAF),RPRC013487),RPRC002420),RPRC011511),(CG17309DmelTK_Csk,RPRC010544)),(((CG5483DmelTKL_LRRK,RPRC008090),RPRC000839),(CG11573DmelTK_DDR,CG8767DmelOther_MOS))),RPRC001940),((((RPRC012934,RPRC014675-6),rlDmelCMGC_MAPK_ERK1),RPRC015450),((EphDmelTK_Eph,RPRC001692),CG11533DmelCK1_TTBK))),((((((RPRC003822,RPRC011049),CG11221DmelOther_NKF1),(CG17090DmelCMGC_DYRK_HIPK,RPRC003671)),RPRC008213),(CG7094DmelCK1_CK1_CK1-A,CaMKIDmelCAMK_CAMK1)),(((((RPRC004886,RPRC011911),RPRC002282),(RPRC007337,RPRC008334)),otkDmelTK_CCK4),CG4410DmelAtypical_ABC1_ABC1-A))))),((((((((((RPRC002012,RPRC002513-RPRC000814),RPRC005941),ballDmelCK1_VRK),((RPRC004234,RPRC010636),ialDmelOther_Aur)),((CG11859DmelAtypical_RIO_RIO2,grpDmelCAMK_CAMKL_CHK1),(CG4588DmelCMGC_RCK_MAK,RPRC008684))),(((((RPRC007432,RPRC011204),RPRC005871),(CG18021DmelCAMK_MLCK,Mekk1DmelSTE_STE11_MEKK4)),((Fps85DDmelTK_Fer,htlDmelTK_FGFR),RPRC009930-1-RPRC013013)),RPRC014924)),((CG3008DmelAtypical_RIO_RIO3,CG3216DmelRGC_RGC),RPRC003744)),(((CG1776DmelCAMK_MLCK,RPRC003276),RPRC001999),RPRC000861-2)),(CG11489DmelCMGC_SRPK,Pkg21DDmelAGC_PKG)),((((((((LIMK1DmelTKL_LISK_LIMK,RPRC007911-RPRC007813),PakDmelSTE_STE20_PAKA),CG4224DmelRGC_RGC),((RPRC006390,RPRC014709),RPRC013306)),(Bub1DmelOther_BUB,CG3277DmelTK_VEGFR)),(((RPRC003907,RPRC014832-RPRC001488),RPRC001226),fs1hDmelAtypical_BRD)),(((((CG7097DmelSTE_STE20_KHS,IlkDmelTKL_MLK_ILK),Dyrk3DmelCMGC_DYRK_DYRK2),(CG1227DmelOther_NAK_MPSK,Cdk7DmelCMGC_CDK_CDK7)),(Cdk9DmelCMGC_CDK_CDK9,ire-1DmelOther_IRE)),(CG5790DmelOther_CDC7,RPRC011628))),(((RPRC004150,RPRC008787),RPRC014715),(RPRC009305,sevDmelTK_Sev))))),(((((((((((((CG11870DmelCAMK_CAMKL_NuaK,RetDmelTK_Ret),(FRAPDmelAtypical_PIKK_FRAP,RPRC003862)),RPRC009518),SAKDmelOther_PLK_SAK),Btk29ADmelTK_Tec),cdc2rkDmelCMGC_CDK_CDK10),((CG1760DmelCAMK_DAPK_DRAK,RPRC009002),RPRC010542)),((((RPRC013423,p38bDmelCMGC_MAPK_p38),CG4549DmelAtypical_PIKK_SMG1),P38cDmelCMGC_MAPK_p38),Gcn2DmelOther_PEK_GCN2)),(((RPRC010134,RPRC012987),RPRC008784),CG2049DmelAGC_PKN)),((((((RPRC008863,RPRC012556),RPRC005095),cdc2cDmelCMGC_CDK_CDC2),RPRC003359-RPRC003363-RPRC003284),((RPRC001953,S6kDmelAGC_RSK_RSK),RPRC007035)),((RPRC005633,TORDmelTK_TK-Unique),RPRC003853))),(((((RPRC007939,RPRC009740),RPRC009327),CG10951DmelOther_NEK_NEK8),(CG9783DmelRGC_RGC,RPRC010221)),(RPRC007336,RPRC013098))),((((((RPRC007441,SlobDmelOther_Slob),CG7125DmelCAMK_PKD),RPRC007221),(RPRC001325,RPRC015332)),RPRC006664),((RPRC006941,gsktDmelCMGC_GSK),RPRC013044))),((((((((((CG18020DmelCAMK_MLCK,frayDmelSTE_STE20_FRAY),RPRC004319),RPRC012995),RPRC004339),(Cdk4DmelCMGC_CDK_CDK4,RPRC006251)),((RPRC014259,Strn-MlckDmelCAMK_MLCK),fuDmelOther_ULK_Fused)),RorDmelTK_Ror),(CG8866DmelOther_ULK_ULK,RPRC012200)),(((RPRC001554-5,RPRC013388),CG14030DmelOther_BUB),RPRC000404)),(((KP78bDmelCAMK_CAMKL_MARK,gwlDmelAGC_MAST_MASTL),RPRC008336),(WSCKDmelTK_TK-Unique,cdiDmelTKL_LISK_TESK))))),(((((((((((CG10673DmelOther_Bud32,Lk6DmelCAMK_MAPKAPK_MNK),Pka-C2DmelAGC_PKA),PhKDmelCAMK_PHK),slprDmelTKL_MLK_MLK),((RPRC009257,RPRC014923),Mkk4DmelSTE_STE7_MEK4)),((RPRC002358,RPRC007991),RPRC009342)),RPRC013175),(((((CaMKIIDmelCAMK_CAMK2,RPRC007535),Pk17EDmelAGC_RSKR),CG2905DmelAtypical_PIKK_TRRAP),(CG1973DmelOther_SCY1,mbtDmelSTE_STE20_PAKB)),(((CG10967DmelOther_ULK_ULK,CG8878DmelCK1_VRK),RPRC013028),(RPRC014191,Takl1DmelTKL_MLK_TAK1)))),RPRC010466),((RPRC013702,SRPKDmelCMGC_SRPK),CG3608DmelAtypical_ABC1_ABC1-B)),(((((((RPRC001102,RPRC008730-RPRC001610),(RPRC004538,RPRC008054)),(CG4945DmelOther_NKF1,Pak3DmelSTE_STE20_PAKA)),RPRC008233),RPRC012856),Pka-C1DmelAGC_PKA),(((CG10522DmelAGC_DMPK_CRIK,InRDmelTK_InsR),(CG7177DmelOther_WNK,cdc2DmelCMGC_CDK_CDC2)),Gyc76CDmelRGC_RGC)))),(((((((BABODmelTKL_STKR_Type1,Pkc53EDmelAGC_PKC_Alpha),RPRC009939),RPRC000184IsoA),RPRC000576),((RPRC008861,witDmelTKL_STKR_Type2),trcDmelAGC_NDR)),(((KP78aDmelCAMK_CAMKL_MARK,RPRC008560),(Pkc98EDmelAGC_PKC_Eta,RPRC002018)),RPRC012932)),MAPk-Ak2DmelCAMK_MAPKAPK_MAPKAPK)),((((((((((((CG9818DmelAGC_YANK,PKA-C3DmelAGC_PKA),RPRC014787-89),RPRC002498),Mpk2DmelCMGC_MAPK_p38),(RPRC008241,inaCDmelAGC_PKC_Alpha)),RPRC014526-7),(((((Drl-2DmelTK_Ryk,PDKDmelAtypical_PDHK_PDHK),RPRC005266),Pk92BDmelSTE_STE11_ASK),CG9374DmelCAMK_CAMKL_LKB),(CG10177DmelCAMK_CAMK-Unique,STLKDmelSTE_STE20_STLK))),((CG7616DmelAtypical_ABC1_ABC1-B,nmoDmelCMGC_MAPK_nmo),RPRC009893)),(((((CG4839DmelAGC_PKG,Taf250DmelAtypical_TAF1),Gyc32EDmelRGC_RGC),(RPRC008551,RPRC010991)),RPRC011822),(PEKDmelOther_PEK_PEK,trblDmelCAMK_Trbl))),(((((CG2309DmelCMGC_MAPK_ERK7,RPRC010541),RPRC005528),RPRC012412),(((RPRC013105,sharkDmelTK_Syk),(RPRC013527,licDmelSTE_STE7_MEK3)),RPRC003281)),((CakiDmelCAMK_CASK,dntDmelTK_Ryk),RPRC006860))),(((((MadmDmelOther_NRBP,ird5DmelOther_IKK),(RPRC005512,RPRC008402)),((RPRC006045,forDmelAGC_PKG),(RPRC011211,bonDmelAtypical_TIF1))),RPRC010713),((CG7028DmelCMGC_DYRK_PRP4,RPRC011265),CG7236DmelCMGC_CDKL))),((((((((CG14305DmelCAMK_TSSK,NrkDmelTK_Musk),(CG8655DmelOther_CDC7,Eip63EDmelCMGC_CDK_PFTAIRE)),CG15072DmelCAMK_CAMKL_QIK),RPRC001119-RPRC04318),(((RPRC000971,SAXDmelTKL_STKR_Type1),(RPRC007546,RPRC010696)),RPRC005491)),Pk34ADmelCMGC_GSK),((((((CG17528DmelCAMK_DCAMKL,CG8565DmelCMGC_SRPK),RPRC003727),CG5169DmelSTE_STE20_YSK),PitslreDmelCMGC_CDK_PITSLRE),PvrDmelTK_VEGFR),RPRC001286)),(((CG11660DmelAtypical_RIO_RIO1,RPRC000798),RPRC000184IsoB),(RPRC002038,RPRC011471))))),RPRC001241)
  tree height = 344.58934423387706

Using strict molecular clock model.
Creating site model.
  4 category discrete gamma with initial shape = 0.5

TreeLikelihood(treeModel) using Java amino acid likelihood core
  Ignoring ambiguities in tree likelihood.
  With 13777 unique site patterns.
Branch rate model used: strictClockBranchRates

Any suggestion?

Best wishes
Jose

[Andrew Rambaut]

Dear Jose,

Try using BEAGLE. If this doesn’t work then contact the Cipres support. This doesn’t look like a BEAST issue.

Best,

Andrew

[Jose Manuel Latorre Estivalis]

Dear Andrew,
Thanks a lot for your reply,
I have tried using BEAGLE in Cipress and the BEAST stops here:

CIPRES_THREADSPP=1
CIPRES_NP=1
running:
beast -beagle_scaling dynamic -threads 1 -beagle_SSE -beagle_instances 1 -beagle_GPU -beagle_cuda infile.xml

Using BEAGLE library v2.1 for accelerated, parallel likelihood evaluation
2009-2013, BEAGLE Working Group - http://beagle-lib.googlecode.com/
Citation: Ayres et al (2012) Systematic Biology 61: 170-173 | doi:10.1093/sysbio/syr100



Random number seed: 1499874544502


Parsing XML file: infile.xml
  File encoding: ISO8859_15
Looking for plugins in /projects/ps-ngbt/backend/comet_workspace/NGBW-JOB-BEAST_TG-9F5FE068B5DF423BBCCA90D1EE4FFF28/plugins
Read alignment: alignment
  Sequences = 438
      Sites = 19965
   Datatype = amino acid
Site patterns 'patterns' created from positions 1-19965 of alignment 'alignment'
  unique pattern count = 13777
Using Yule prior on tree
Creating the tree model, 'treeModel'
  initial tree topology = (((((((((((((((((((CG2049DmelAGC_PKN,RPRC011204),SNF1ADmelCAMK_CAMKL_AMPK),(RPRC009257,RPRC010466)),((MadmDmelOther_NRBP,RPRC001692),Lk6DmelCAMK_MAPKAPK_MNK)),CG5169DmelSTE_STE20_YSK),RPRC009740),((((MAPk-Ak2DmelCAMK_MAPKAPK_MAPKAPK,phlDmelTKL_RAF_RAF),hopDmelTK_Jak),(RPRC007432,RPRC014526-7)),((CG5483DmelTKL_LRRK,tlkDmelOther_TLK),CG4839DmelAGC_PKG))),((AlkDmelTK_ALK,RPRC002513-RPRC000814),(RPRC013702,auxillinDmelOther_NAK_GAK))),(((((Pka-C2DmelAGC_PKA,RPRC013098),AblDmelTK_Abl),RPRC007939),CG8866DmelOther_ULK_ULK),RPRC007991)),((((((CG4945DmelOther_NKF1,sevDmelTK_Sev),Bub1DmelOther_BUB),(CG14217DmelSTE_STE20_TAO,RPRC009930-1-RPRC013013)),RPRC013044),((CG3277DmelTK_VEGFR,PitslreDmelCMGC_CDK_PITSLRE),(RPRC007546,RPRC011049))),((CG2905DmelAtypical_PIKK_TRRAP,RPRC011911),(RPRC012077,RPRC014709)))),(((((((((RPRC013306,fs1hDmelAtypical_BRD),ire-1DmelOther_IRE),RPRC002914),((RPRC000404,RPRC008402),Pkc98EDmelAGC_PKC_Eta)),(NrkDmelTK_Musk,RPRC005800)),((((CG11870DmelCAMK_CAMKL_NuaK,RPRC007336),(RPRC005266,tkvDmelTKL_STKR_Type1)),(CG8485DmelCAMK_CAMKL_SNRK,Pk61CDmelAGC_PDK1)),(RPRC013655,ksrDmelTKL_RAF_KSR))),((RPRC004339,RPRC008730-RPRC001610),poloDmelOther_PLK_PLK1)),(CG17698DmelOther_CAMKK_Meta,CG8726DmelOther_Slob)),((((CG7643DmelOther_TTK,RPRC009518),RPRC004857),((Cdk4DmelCMGC_CDK_CDK4,RPRC010713),lokDmelCAMK_RAD53)),((CG4224DmelRGC_RGC,RPRC007843),(Fak56DDmelTK_FAK,RPRC006045))))),(((((PvrDmelTK_VEGFR,S6kDmelAGC_RSK_RSK),CG6114DmelCAMK_CAMKL_BRSK),(Pk34ADmelCMGC_GSK,RPRC004538)),(((RPRC003281,Taf250DmelAtypical_TAF1),RPRC003727),FRAPDmelAtypical_PIKK_FRAP)),((EphDmelTK_Eph,RPRC009035-33-RPRC008857),RPRC013126))),((((((((((CG17309DmelTK_Csk,CG7156DmelAGC_RSKL),(RPRC006429,RPRC008560)),RPRC005688),bonDmelAtypical_TIF1),(((RPRC001641,RPRC010540),RPRC008054),Pk92BDmelSTE_STE11_ASK)),RPRC000861-2),(Cdk9DmelCMGC_CDK_CDK9,RPRC006659)),RPRC005633),((((((RPRC011265,SlobDmelOther_Slob),RPRC003359-RPRC003363-RPRC003284),Gcn2DmelOther_PEK_GCN2),((RPRC006390,RPRC015450),RPRC007812)),RPRC003822),(((Fps85DDmelTK_Fer,RPRC001740),RPRC006941),S6kIIDmelAGC_RSK_p70))),((((((Btk29ADmelTK_Tec,IlkDmelTKL_MLK_ILK),RPRC000321),sharkDmelTK_Syk),nmoDmelCMGC_MAPK_nmo),RPRC013423),(((((CG11660DmelAtypical_RIO_RIO1,RPRC001999),RPRC001226),RPRC000184IsoA),(Dyrk3DmelCMGC_DYRK_DYRK2,grpDmelCAMK_CAMKL_CHK1)),RPRC012179)))),(((((((((CG6535DmelAtypical_PIKK_ATM,RPRC007079),KP78aDmelCAMK_CAMKL_MARK),RPRC007337),RPRC002358),((RPRC009939,RPRC012309),witDmelTKL_STKR_Type2)),(CG11489DmelCMGC_SRPK,Pkg21DDmelAGC_PKG)),((((CG17528DmelCAMK_DCAMKL,RPRC014259),CG1227DmelOther_NAK_MPSK),Takl2DmelTKL_MLK_TAK1),(RPRC009342,btDmelCAMK_MLCK))),(((((CG9962DmelCK1_CK1_CK1-Unclassified,Cdk8DmelCMGC_CDK_CDK8),CG12147DmelCK1_CK1_CK1-Unclassified),CG10177DmelCAMK_CAMK-Unique),(RPRC010134,licDmelSTE_STE7_MEK3)),CG8789DmelTKL_MLK_LZK)),(((((RPRC009002,msnDmelSTE_STE20_MSN),RPRC009893),RPRC003671),mei-41DmelAtypical_PIKK_ATR),(RPRC005095,dntDmelTK_Ryk)))),((((((((CG6498DmelAGC_MAST_MAST,RPRC001940),RPRC010542),(CG7094DmelCK1_CK1_CK1-A,RPRC002851)),RPRC009810),((Pk17EDmelAGC_RSKR,RPRC012489),PKCdeltaDmelAGC_PKC_Delta)),KP78bDmelCAMK_CAMKL_MARK),((((CakiDmelCAMK_CASK,DoaDmelCMGC_CLK),CG9746DmelOther_VPS15),Cad96CaDmelTK_TK-Unique),(CG7616DmelAtypical_ABC1_ABC1-B,RPRC009486))),((((RPRC010991,RPRC011822),CaMKIIDmelCAMK_CAMK2),RPRC014924),RPRC014832-RPRC001488))),(((((((((CG4410DmelAtypical_ABC1_ABC1-A,RPRC002038),(CG8655DmelOther_CDC7,HaspinDmelOther_Haspin)),(RPRC014583-92,RPRC015112)),ninaCDmelSTE_STE20_NinaC),RPRC011511),CG3105DmelCAMK_CAMKL_PASK),CG15072DmelCAMK_CAMKL_QIK),(((((RPRC013140,RPRC013527),SAKDmelOther_PLK_SAK),RPRC011471),RPRC013028),(AckDmelTK_Ack,CG17090DmelCMGC_DYRK_HIPK))),((((((CG7125DmelCAMK_PKD,hepDmelSTE_STE7_MEK7),PDKDmelAtypical_PDHK_PDHK),Gyc76CDmelRGC_RGC),((CG11221DmelOther_NKF1,RPRC015332),(Myt1DmelOther_WEE,RPRC003862))),RPRC000798),((((RPRC001286,RPRC011597),(otkDmelTK_CCK4,sggDmelCMGC_GSK)),(RPRC012556,RPRC013601)),EgfrDmelTK_EGFR)))),(((((((((CG11228DmelSTE_STE20_MST,RPRC003040),(RPRC001078,RPRC007221)),rokDmelAGC_DMPK_ROCK),(Cdk5DmelCMGC_CDK_CDK5,Tak1DmelTKL_MLK_TAK1)),(Akt1DmelAGC_Akt,CG9222DmelCAMK_TSSK)),((((CaMKIDmelCAMK_CAMK1,Strn-MlckDmelCAMK_MLCK),PakDmelSTE_STE20_PAKA),RPRC014191),(RPRC000863-4,RPRC002282))),((RPRC012412,RPRC013175),CG12069DmelAGC_PKA)),(((drlDmelTK_Ryk,ird5DmelOther_IKK),RPRC013487),CkIalphaDmelCK1_CK1_CK1-A)),(((((((CG8878DmelCK1_VRK,RPRC005609),RPRC003670),RPRC008241),(((RPRC001102,RPRC004234),RPRC010391),fuDmelOther_ULK_Fused)),PEKDmelOther_PEK_PEK),((((CG7177DmelOther_WNK,slprDmelTKL_MLK_MLK),(CkIIalphaDmelCMGC_CK2,gishDmelCK1_CK1_CK1-G)),gwlDmelAGC_MAST_MASTL),(BABODmelTKL_STKR_Type1,RPRC009634))),((((((RPRC001953,RPRC009327),CG7236DmelCMGC_CDKL),(PR2DmelTK_Ack,RPRC003853)),(RPRC005491,mnbDmelCMGC_DYRK_DYRK1)),((CG11859DmelAtypical_RIO_RIO2,RPRC002012),CG18020DmelCAMK_MLCK)),((((RPRC005528,ik2DmelOther_IKK),RPRC007911-RPRC007813),CG1776DmelCAMK_MLCK),RPRC008213))))),(((((((((((((((RPRC004230,cdc2rkDmelCMGC_CDK_CDK10),CG4629DmelCAMK_CAMKL_NIM1),RPRC007535),(CG9374DmelCAMK_CAMKL_LKB,TORDmelTK_TK-Unique)),((CG18021DmelCAMK_MLCK,RPRC008233),(InRDmelTK_InsR,ialDmelOther_Aur))),((CG11533DmelCK1_TTBK,RPRC007732),RPRC002420)),(((((RPRC002498,RPRC006894),Cdk7DmelCMGC_CDK_CDK7),RPRC003276),(CG10967DmelOther_ULK_ULK,CG4523DmelOther_NKF2)),(CG3216DmelRGC_RGC,RPRC006251))),(((CG1344DmelOther_SCY1,CG7097DmelSTE_STE20_KHS),trblDmelCAMK_Trbl),CG5790DmelOther_CDC7)),(((((CG14030DmelOther_BUB,RPRC000167),CG1760DmelCAMK_DAPK_DRAK),htlDmelTK_FGFR),((Pka-C1DmelAGC_PKA,RPRC000576),RPRC009305)),((Eip63EDmelCMGC_CDK_PFTAIRE,RPRC008551),gekDmelAGC_DMPK_GEK))),(((((RPRC008863,RPRC010541),Pak3DmelSTE_STE20_PAKA),aPKCDmelAGC_PKC_Iota),((CG3008DmelAtypical_RIO_RIO3,RetDmelTK_Ret),RPRC007035)),(LIMK1DmelTKL_LISK_LIMK,STLKDmelSTE_STE20_STLK))),(((((((((CG2577DmelCK1_CK1_CK1-Unclassified,RPRC012957),Mpk2DmelCMGC_MAPK_p38),(RPRC005871,WSCKDmelTK_TK-Unique)),Gprk1DmelAGC_GRK_BARK),RPRC001554-5),(((JIL1DmelAGC_RSK_MSK,RPRC004552),(RPRC001119-RPRC04318,RPRC008861)),(RPRC010221,btlDmelTK_FGFR))),(RPRC011211,RPRC012856)),((((((RPRC012987,RPRC015071),SAXDmelTKL_STKR_Type1),RPRC005941),RPRC012995),RPRC008334),RorDmelTK_Ror)),((((((CG8173DmelOther_TOPK,RPRC013388),RPRC013105),bskDmelCMGC_MAPK_JNK),pllDmelTKL_IRAK),inaCDmelAGC_PKC_Alpha),(Mekk1DmelSTE_STE11_MEKK4,trcDmelAGC_NDR)))),(((((((CG10673DmelOther_Bud32,RPRC003744),mbtDmelSTE_STE20_PAKB),RPRC001869),CG4527DmelSTE_STE20_SLK),CG8767DmelOther_MOS),CG4290DmelCAMK_CAMKL_QIK),(((((RPRC010636,Src64BDmelTK_Src_Src-Unclassified),RPRC007591),CG7597DmelCMGC_CDK_CRK7),(PhKDmelCAMK_PHK,RPRC004886)),(RPRC000839,RPRC012200)))),((((((((((CG1951DmelOther_SCY1,RPRC008787),(Gprk2DmelAGC_GRK_GRK,RPRC010544)),((Pkc53EDmelAGC_PKC_Alpha,RPRC014675-6),Dsor1DmelSTE_STE7_MEK1)),((Par-1DmelCAMK_CAMKL_MARK,weeDmelOther_WEE),cdc2cDmelCMGC_CDK_CDC2)),((((CG4041DmelOther_TBCK,forDmelAGC_PKG),(RPRC005512,RPRC006664)),((CG4549DmelAtypical_PIKK_SMG1,RPRC000333),RPRC004775)),RPRC008336)),(CG7028DmelCMGC_DYRK_PRP4,RPRC001637-5-RPRC005426-7)),((RPRC004319,gsktDmelCMGC_GSK),Mkk4DmelSTE_STE7_MEK4)),((((((CG2309DmelCMGC_MAPK_ERK7,RPRC014923),(CG9818DmelAGC_YANK,RPRC009624)),RPRC000971),(RPRC012932,SRPKDmelCMGC_SRPK)),(RPRC003907,RPRC010696)),(((((RPRC005685,frayDmelSTE_STE20_FRAY),CG14305DmelCAMK_TSSK),RPRC008734),CG10738DmelRGC_RGC),(((CG11573DmelTK_DDR,p38bDmelCMGC_MAPK_p38),wtsDmelAGC_NDR),Src42ADmelTK_Src_Frk)))),((((((((RPRC006860,pngDmelOther_Other-Unique),putDmelTKL_STKR_Type2),RPRC011628),smi35ADmelCMGC_DYRK_DYRK2),RPRC008684),RPRC004150),((CG3608DmelAtypical_ABC1_ABC1-B,P38cDmelCMGC_MAPK_p38),RPRC004208)),(((CG14163DmelOther_SCY1,RPRC008784),(RPRC005429-,RPRC007441)),(RPRC012934,dcoDmelCK1_CK1_CK1-D)))),((((((CG1973DmelOther_SCY1,RPRC001790),RPRC014787-89),RPRC002018),((RPRC008090,Takl1DmelTKL_MLK_TAK1),aurDmelOther_Aur)),(CG8565DmelCMGC_SRPK,RPRC001666)),(((NakDmelOther_NAK_BIKE,ballDmelCK1_VRK),(Nek2DmelOther_NEK_NEK2,RPRC006548)),CG10522DmelAGC_DMPK_CRIK)))),((((((RPRC015063,cdc2DmelCMGC_CDK_CDC2),CG10951DmelOther_NEK_NEK8),(PKA-C3DmelAGC_PKA,cdiDmelTKL_LISK_TESK)),(RPRC001325,TieDmelTK_TK-Unique)),((CG9783DmelRGC_RGC,RPRC014715),CG4588DmelCMGC_RCK_MAK)),(Drl-2DmelTK_Ryk,rlDmelCMGC_MAPK_ERK1))),((Gyc32EDmelRGC_RGC,RPRC000184IsoB),CG6800DmelCMGC_CDK_CDK-Unclassified))),RPRC001241)
  tree height = 414.0863631835545
Using strict molecular clock model.
Creating site model: 
  4 category discrete gamma with initial shape = 0.5
Using BEAGLE TreeLikelihood
  Branch rate model used: strictClockBranchRates

I used the same input file. A STDERR file was generated and saids:

CUDA error: "Out of memory" from file <GPUInterfaceCUDA.cpp>, line 432.
srun: error: comet-30-09: task 0: Exited with exit code 255


Do you think this is still a problem of Cipres or I am doing something wrong?

Thanks a lot for your help

Best wishes
Jose

[Miller, Mark]

Hi Jose,

You can send me the file _jobinfo.txt if you need support from us.

Best

Mark

[Jose Manuel Latorre Estivalis]

Hi Mark
The file jobinfo.txt saids:

Task\ label=Vamos_con_Beagle
Task\ ID=1237547
Tool=BEAST_TG
created\ on=2017-07-12 08:46:44.0
JobHandle=NGBW-JOB-BEAST_TG-9F5FE068B5DF423BBCCA90D1EE4FFF28
resource=comet
User\ ID=81314
User\ Name=josmantorres
email=josman...@gmail.com

Output=(all_results,*,UNKNOWN,UNKNOWN,UNKNOWN)
ChargeFactor=1.000000
cores=1
JOBID=10170280

I hope you can help me.
Thanks again for your help
Best,
Jose

[Yan Wang]

Hi Jose,

I have got the same problem with CUDA "Out of memory" error. May I know is it fixed now?

Best,

Yan