New Version: Fatal Error: java.lang.NumberFormatException: For input string: "?"

[Cat]

Dear Maxent users,

I have been using Maxent now for about a year and am pretty familiar
with how it works. I have run countless models through the algorithm
without any fatal problems (or at least in the begining, none that I
couldn't troubleshoot myself). I am in the final steps of submitting
my thesis and just wanted to double check and re-run a couple of
models and now, some of them, simply won't run all the way through.

I get this message: Fatal Error: java.lang.NumberFormatException: For
input string: "?"
I do not have an empty ? column, so im not sure to what exactly its
reacting too.
Furthermore, because I am running 10 subsamples for each analysis
(60:40 data split for building:testing), the algorithm with abruptly
stop at a RANDOM point along its 10 subset course ( sometime Ill get
all the way to subset 9 and it will crash!)

I have run these models before, with almost identical data (I
repartitioned it more recently, but the categories and averages come
out to approximately the same values) and identical headers.

I am only modelling one species...so species name shouldn't be the
problem...

Here is the log file for the beginning and for the last 9 iterations
(I picked a max of 1000 iterations):

Wed Apr 21 15:46:54 EDT 2010
MaxEnt version 3.3.2
Reading file xBackground_1.csv
readGrid: max memory 532742144, total allocated 5177344, free 2009752,
used 3167592, increment 3167592
Reading samples from xBLTU_1.csv
Read samples: max memory 532742144, total allocated 6959104, free
1200072, used 5759032, increment 2591440
Making features
makeFeatures: max memory 532742144, total allocated 27701248, free
6911664, used 20789584, increment 15030552
Command line used:
Command line to repeat: java density.MaxEnt nowarnings noprefixes
responsecurves jackknife outputdirectory=Z:\FastGIS\MAXENT\x1results
projectionlayers=Z:\FastGIS\MAXENT\x1ascii samplesfile=Z:\FastGIS
\MAXENT\x1input\xBLTU_1.csv environmentallayers=Z:\FastGIS\MAXENT
\x1input\xBackground_1.csv randomseed nowriteclampgrid
randomtestpoints=40 maximumbackground=16666 replicates=10
replicatetype=subsample writebackgroundpredictions
noaddsamplestobackground writeplotdata nodoclamp nooutputgrids
appendtoresultsfile maximumiterations=1000 nocache verbose
allowpartialdata
Species: BLTU_0 BLTU_1 BLTU_2 BLTU_3 BLTU_4 BLTU_5 BLTU_6 BLTU_7
BLTU_8 BLTU_9
Layers: xalvar1 xcb1 xcrop1 xforest1 xpast1 xplant1 xprec1 xrock1
xtmax1 xtrd1 xtri1 xurban1 xwater1 xwetl1
Layertypes: Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Continuous
responsecurves: true
jackknife: true
outputdirectory: Z:\FastGIS\MAXENT\x1results
projectionlayers: Z:\FastGIS\MAXENT\x1ascii
samplesfile: Z:\FastGIS\MAXENT\x1input\xBLTU_1.csv
environmentallayers: Z:\FastGIS\MAXENT\x1input\xBackground_1.csv
randomseed: true
writeclampgrid: false
randomtestpoints: 40
maximumbackground: 16666
replicates: 10
replicatetype: subsample
writebackgroundpredictions: true
addsamplestobackground: false
writeplotdata: true
doclamp: false
outputgrids: false
appendtoresultsfile: true
maximumiterations: 1000
cache: false
verbose: true
allowpartialdata: true

getSamples: max memory 532742144, total allocated 27701248, free
6623480, used 21077768, increment 288184
BLTU_0:
Regularization values: linear/quadratic/product: 0.050, categorical:
0.250, threshold: 1.000, hinge: 0.500
Time since start: 1.662
370 samples
Density: max memory 532742144, total allocated 47091712, free 2760472,
used 44331240, increment 23253472
linearPredictor: max memory 532742144, total allocated 47091712, free
2627128, used 44464584, increment 133344
FeaturedSpace: max memory 532742144, total allocated 47091712, free
2625064, used 44466648, increment 2064
Sequential: max memory 532742144, total allocated 47091712, free
2596728, used 44494984, increment 28336
Initial loss: 9.721125994942152
Initial test loss: 9.721125994942152
Updating 119 features
increaseLambda: 0.17 0.170000
0: time = 0.170000 loss = 9.711597 testLoss 9.712174
(20.98848533630371<xtmax1) lambda = 0.0365
alpha = 0.036483 lossBound = -0.197451 W1 = 0.665200 N1 = 0.935135
deltaLoss = -0.009529
Updating 119 features
increaseLambda: 0.339 0.169000
1: time = 0.339000 loss = 9.702546 testLoss 9.703688
(20.98848533630371<xtmax1) lambda = 0.0722
alpha = 0.035753 lossBound = -0.187922 W1 = 0.673115 N1 = 0.935135
deltaLoss = -0.009051
Updating 119 features
increaseLambda: 0.505 0.166000

2...990 iterations later

991: time = 141.441000 loss = 4.494521 testLoss -25.575393
'xprec1__rev lambda = 3,357.5841
alpha = 9.088997 lossBound = -0.000732 W1 = 0.001217 N1 = 0.002960
deltaLoss = -0.007143
Updating 6 features
increaseLambda: 141.565 0.124000
992: time = 141.565000 loss = 4.491778 testLoss -25.572250
(35.88983345031738<xurban1) lambda = -50.3031
alpha = -0.866865 lossBound = -0.002743 W1 = 0.005405 N1 = 0.002703
deltaLoss = -0.002743
Updating 9 features
NewtonStep: 141.666 0.101000
increaseLambda: 141.689 0.023000
Undoing: newLoss 4.495050462123524, oldLoss 4.491778477026521,
deltaLossBound -7.323752673996915E-4
increaseLambda: 141.712 0.023000
Search: 141.716 0.004000
increaseLambda: 141.739 0.023000
993: time = 141.739000 loss = 4.484636 testLoss -25.666099
'xprec1__rev lambda = 3,366.6731
alpha = 9.088997 lossBound = -0.000732 W1 = 0.001217 N1 = 0.002960
deltaLoss = -0.007143
Updating 6 features
increaseLambda: 141.862 0.123000
994: time = 141.862000 loss = 4.481893 testLoss -25.666480
(59.73135566711426<xurban1) lambda = -4.3357
alpha = -0.866865 lossBound = -0.002743 W1 = 0.005405 N1 = 0.002703
deltaLoss = -0.002743
Updating 9 features
NewtonStep: 141.963 0.101000
increaseLambda: 141.987 0.024000
Undoing: newLoss 4.485164572006651, oldLoss 4.481892586909649,
deltaLossBound -7.323752673996915E-4
increaseLambda: 142.009 0.022000
Search: 142.013 0.004000
increaseLambda: 142.037 0.024000
995: time = 142.037000 loss = 4.474750 testLoss -25.760329
'xprec1__rev lambda = 3,375.7621
alpha = 9.088997 lossBound = -0.000732 W1 = 0.001217 N1 = 0.002960
deltaLoss = -0.007143
Updating 6 features
increaseLambda: 142.161 0.124000
996: time = 142.161000 loss = 4.472007 testLoss -25.760711
(59.73135566711426<xurban1) lambda = -5.2026
alpha = -0.866865 lossBound = -0.002743 W1 = 0.005405 N1 = 0.002703
deltaLoss = -0.002743
Time since start: 144.141
Updating 10 features
NewtonStep: 142.262 0.101000
increaseLambda: 142.285 0.023000
Undoing: newLoss 4.47527868188978, oldLoss 4.472006696792777,
deltaLossBound -7.323752673996915E-4
increaseLambda: 142.308 0.023000
Search: 142.312 0.004000
increaseLambda: 142.335 0.023000
997: time = 142.336000 loss = 4.464864 testLoss -25.854560
'xprec1__rev lambda = 3,384.8511
alpha = 9.088997 lossBound = -0.000732 W1 = 0.001217 N1 = 0.002960
deltaLoss = -0.007143
Updating 6 features
increaseLambda: 142.46 0.124000
998: time = 142.460000 loss = 4.462121 testLoss -25.854941
(59.73135566711426<xurban1) lambda = -6.0695
alpha = -0.866865 lossBound = -0.002743 W1 = 0.005405 N1 = 0.002703
deltaLoss = -0.002743
Updating 9 features
NewtonStep: 142.561 0.101000
increaseLambda: 142.584 0.023000
Undoing: newLoss 4.465392791772903, oldLoss 4.462120806675901,
deltaLossBound -7.323752673996915E-4
increaseLambda: 142.607 0.023000
Search: 142.611 0.004000
increaseLambda: 142.635 0.024000
999: time = 142.635000 loss = 4.454978 testLoss -25.948790
'xprec1__rev lambda = 3,393.9401
alpha = 9.088997 lossBound = -0.000732 W1 = 0.001217 N1 = 0.002960
deltaLoss = -0.007143
1000: time = 142.644000 loss = 4.454978 testLoss -25.948790
Resulting gain: 5.266148067506945
Time since start: 146.18
Fatal Error: java.lang.NumberFormatException: For input string: "?"
java.lang.NumberFormatException: For input string: "?"
at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
at java.lang.Double.parseDouble(Unknown Source)
at density.Project$5.process(Project.java:496)
at density.Csv.apply(Csv.java:158)
at density.Project.readCumulativeIndex(Project.java:493)
at density.Runner.writeCumulativeIndex(Runner.java:1831)
at density.Runner.start(Runner.java:464)
at density.GUI$7.construct(GUI.java:319)
at density.SwingWorker$2.run(SwingWorker.java:108)
at java.lang.Thread.run(Unknown Source)

Any comments/ suggestions would be most helpfull!!
Thanks for your time!!

Sincerely,
-Catherine

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[A.Donaldson]

Hello Cat,

I had this same problem of the "Fatal Error: java.lang.NumberFormatException: For input string:" i fixed it by reducing the size of the environmental file. My file was 3,5GBs and i clipped in arcmap using "clip" tool,  to a specific area of my research. This worked straight away.