error while running fastml

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hello, I am running fastml to develop phylogenetic tree but its showing error and no output is being generated. The command use is perl FastML_Wrapper.pl --MSA_File PF05505_EBOLA_pfam.txt --seqType AA --outdir /home/nsm/k/kx/kxj190026/molevol/ The error: outDir: /home/nsm/k/kx/kxj190026/molevol/ SubMatrix=JTT (default) Copy and analyse MSA: /home/nsm/k/kx/kxj190026/molevol/PF05505_EBOLA_pfam.txt LOG: /home/nsm/k/kx/kxj190026/molevol/FastML_log.log cd /home/nsm/k/kx/kxj190026/molevol/; /home/nsm/k/kx/kxj190026/molevol/FastML.v3.11/www/fastml/../../programs/fastml/fastml -s /home/nsm/k/kx/kxj190026/molevol/PF05505_EBOLA_pfam.txt -mj -qf -g > /home/nsm/k/kx/kxj190026/molevol/fastml.std --- Iter=0 logL=-5140.31 LikelihoodLast was not sent to bblEM --- Iter=1 logL=-5132.6 LikelihoodLast was not sent to bblEM --- Iter=2 logL=-5128.84 LikelihoodLast was not sent to bblEM --- Iter=3 logL=-5126.4 LikelihoodLast was not sent to bblEM --- Iter=4 logL=-5124.6 LikelihoodLast was not sent to bblEM --- Iter=5 logL=-5123.19 LikelihoodLast was not sent to bblEM --- Iter=6 logL=-5122.05 LikelihoodLast was not sent to bblEM --- Iter=7 logL=-5121.13 LikelihoodLast was not sent to bblEM --- Iter=8 logL=-5120.36 LikelihoodLast was not sent to bblEM --- Iter=9 logL=-5119.73 LikelihoodLast was not sent to bblEM --- Iter=0 logL=-5115.69 LikelihoodLast was not sent to bblEM --- Iter=1 logL=-5114.06 LikelihoodLast was not sent to bblEM --- Iter=2 logL=-5112.98 LikelihoodLast was not sent to bblEM --- Iter=3 logL=-5112.16 LikelihoodLast was not sent to bblEM --- Iter=4 logL=-5111.52 LikelihoodLast was not sent to bblEM --- Iter=5 logL=-5111 LikelihoodLast was not sent to bblEM --- Iter=6 logL=-5110.57 LikelihoodLast was not sent to bblEM --- Iter=7 logL=-5110.21 LikelihoodLast was not sent to bblEM --- Iter=8 logL=-5109.92 LikelihoodLast was not sent to bblEM --- Iter=9 logL=-5109.68 LikelihoodLast was not sent to bblEM --- Iter=0 logL=-5108.26 LikelihoodLast was not sent to bblEM --- Iter=1 logL=-5107.66 LikelihoodLast was not sent to bblEM --- Iter=2 logL=-5107.23 LikelihoodLast was not sent to bblEM --- Iter=3 logL=-5106.91 LikelihoodLast was not sent to bblEM --- Iter=4 logL=-5106.65 LikelihoodLast was not sent to bblEM --- Iter=5 logL=-5106.44 LikelihoodLast was not sent to bblEM --- Iter=6 logL=-5106.26 LikelihoodLast was not sent to bblEM --- Iter=7 logL=-5106.12 LikelihoodLast was not sent to bblEM --- Iter=8 logL=-5106 LikelihoodLast was not sent to bblEM --- Iter=9 logL=-5105.91 LikelihoodLast was not sent to bblEM --- Iter=0 logL=-5105.29 LikelihoodLast was not sent to bblEM --- Iter=1 logL=-5105.02 LikelihoodLast was not sent to bblEM --- Iter=2 logL=-5104.84 LikelihoodLast was not sent to bblEM --- Iter=3 logL=-5104.69 LikelihoodLast was not sent to bblEM --- Iter=4 logL=-5104.58 LikelihoodLast was not sent to bblEM --- Iter=5 logL=-5104.49 LikelihoodLast was not sent to bblEM --- Iter=6 logL=-5104.41 LikelihoodLast was not sent to bblEM --- Iter=7 logL=-5104.35 LikelihoodLast was not sent to bblEM --- Iter=8 logL=-5104.3 LikelihoodLast was not sent to bblEM --- Iter=0 logL=-5104.11 LikelihoodLast was not sent to bblEM --- Iter=1 logL=-5103.99 LikelihoodLast was not sent to bblEM --- Iter=2 logL=-5103.9 LikelihoodLast was not sent to bblEM --- Iter=3 logL=-5103.83 LikelihoodLast was not sent to bblEM --- Iter=4 logL=-5103.77 LikelihoodLast was not sent to bblEM --- Iter=5 logL=-5103.73 LikelihoodLast was not sent to bblEM cd /home/nsm/k/kx/kxj190026/molevol/; perl /home/nsm/k/kx/kxj190026/molevol/FastML.v3.11/www/fastml/IndelReconstruction_Wrapper.pl --MSA_File /home/nsm/k/kx/kxj190026/molevol/PF05505_EBOLA_pfam.txt --Tree_File /home/nsm/k/kx/kxj190026/molevol/tree.newick.txt --outDir /home/nsm/k/kx/kxj190026/molevol/ --seqType aa --indelCutOff 0.5 > /home/nsm/k/kx/kxj190026/molevol//IndelReconstruction.log Seq /home/nsm/k/kx/kxj190026/molevol/PF05505_EBOLA_pfam.txt numberOfSeqs=4 seqLen=716

Step (1) readSequenceIntoGaps... All MSA gaps are sorted by coordinates Sort by: I =(i1,i2), K =(k1,k2), I<K iff i1<k1 or i1=k1 and i2<k2

There are 20 gaps

Step (2) delimitationOfCharacters... Simple Coding (SIC) Finding the required positions(=characters) in the coded sequence The number of characters <= the number of found gaps (each character may include several gaps)

There were 20 characters

Step (3) determinationCharacterState... WARN: compute correlatins for co-Loss, printComputedCorrelationsData() is problematic (not all pair will have both co-gain and co-loss defined) WARN: compute correlatins for co-Loss, printComputedCorrelationsData() is problematic (not all pair will have both co-gain and co-loss defined) +=============================================================+

• The gainLoss project:
• Analysis of Phyletic Patterns in a Likelihood Framework
• Version: gainLoss.VR01.266 - last updated 14.10.2013
• Ofir Cohen - [email protected] +=============================================================+

---------------------- THE PARAMETERS ---------------------------- Likelihood computation is performed while acounting for un-oberved data With min number of presences('1's)= 1 With min number of absences('0's)= 0 'Reversible'(Root.freq==stationary.freq) model is used RootFreq EQ stationary (taken from each sp - gain/(gain+loss) ) inTree file: /home/nsm/k/kx/kxj190026/molevol/tree.newick.txt.ForIndelReconstruction inSeq file: /home/nsm/k/kx/kxj190026/molevol/IndelsReconstruction//PF05505_EBOLA_pfam.indelOutputFastaFile log: RESULTS//log.txt with level= 5 Optimization of the model parmeters is performed rate inference method is: empirical Bayesian estimate using a Gamma prior distribution with: 4 discrete categories branch lengths are not optimized rate4site is calculated calculePosteriorExpectationOfChange is done Analytically

startSequenceContainer numberOfSeqs=4 seqLen=20 Num of zeros=60 Num of ones=36 Num of unKnowns=16

startStochasticProcess...

InitGainLossByEmpiricalFreq: freq 1=init_gain= 0.3125 rateDist GAMMA with: initAlphaRate=0.5 and _numberOfRateCategories= 4 Stochastic process normalized with norm_factor=0.429688 startStochasticProcess SimpleGamma of 4 categories... with gain=0.3125 loss=0.6875 root(1)=0.2 Stochastic process 'simple' normalized with norm_factor=0.429688

startingEvolTreeTopology... default rooting used, root name is N1 sons of root are: S2 S4 N2 unObservableData object initialized with number of unObservable patterns= 1 The Tree Likelihood AllPosAlphTheSame is -37.721 Starting normalizeQandTree...(so that sumQii=1 (or weighted ave. of sunOii's for many Qs)) Q were multiplied by 1 The Tree Likelihood AllPosAlphTheSame is -37.721 AlphaRate 0.5 Gain 0.727273 Loss 1.6 Gain/Loss ratio= 0.454545 Stationary '1' Freq at the root (g/(g+l) = 0.3125 Total branch lengths:5.40937

Starting MaxParsimonyChange... MaxParsimony with costMatrix - gainLossRatio 1:2 Cost of tree is 32 (with 20 events) Gain=12 Losses=8 TIME = 0.0166667 minutes

*** Start Optimizations

WARN: no branch length estimation is performed with too few positions =20

WARN: Skip MultipleAllBranchesByFactorAtStart with too few number of positions 20 multipleAllBranchesByFactorAtStartByMaxParsimonyCost Total branch lengths: 1 with respect to costOfTreeMP 20

Starting optimizations: maxNumIterations=1

######### optimization starting epsilonCycle=5 maxNumIterations=1 start optimization with L= -48.5956

------ Model+BBL iter=1

optimization starting- epsilonOptParam=0.04999 epsilonOptIter= 0.14997, MaxNumIterations=1

start optimization with: L= -48.5956 gainLossRatio= 0.454545 gain= 0.727273 loss= 1.6 Alpha= 0.5

---- iter=1 currBestL= -29.3531 GainLossRatio= 0.0125557 currBestL= -27.9035 Alpha= 94.0399 Too many iterations in optimizeGainLossModel. Iter= 2 Last optimized parameters are used. iter=2

Model optimization over with: Gain 0.112052 Loss 40.3226 Gain/Loss ratio= 0.00277889 AlphaRateRate 94.0399 updated likelihood (after optimizeParameters)= -27.9035 Model optimization RUNNING TIME = 0 minutes

Too many=1 iterations in Model+BBL. Last optimized parameters are used. Optimization RUNNING TIME = 0 minutes

Best likelihood after optimization=-27.9035

TIME = 0 minutes

Starting normalizeQandTree...(so that sumQii=1 (or weighted ave. of sunOii's for many Qs)) Q were multiplied by 1 Tree branches multi by 1 The Tree Likelihood AllPosAlphTheSame is -27.9035 AlphaRate 94.0399 Gain 0.506278 Loss 40.3226 Gain/Loss ratio= 0.0125557 Stationary '1' Freq at the root (g/(g+l) = 0.0124 Total branch lengths:1

WARN: distanceFromRootForRecent=1, distanceFromNearestOTUForRecent=0.000001 are not estimated Starting printLofPos...

Starting rate4site... Running rate4site... perform computeEB_EXP_siteSpecificRate... while computing posteriorProb PerCategory PerPosition computeRate4site RUNNING TIME = 0 minutes TIME = 0 minutes

Starting calculePosteriorExpectationOfChange...

Computation stochastic mapping Computation performed analytically for rate 0.872149 Computation performed analytically for rate 0.963545 Computation performed analytically for rate 1.03039 Computation performed analytically for rate 1.13391 TIME = 0 minutes

Mean values Gain=1.44782 Loss=0.491302 Median values Gain=1.44974 Loss=0.489805

TIME = 0 minutes (calculePosteriorExpectationOfChange)

Starting ancestralReconstructorBasedOnJoint... computeAncestralPosterior (take into acount joint probabilty)... TIME = 0 minutes

I don't know whether its correct. Since in the beginning its showing error as likelihood last was not sent to bblem