delt0r
commented
11 years ago This is a known issue. In fact just about all the issues are the same section of code. I am working on it right now.
Closed szpiech closed 11 years ago
delt0r
commented
11 years ago This is a known issue. In fact just about all the issues are the same section of code. I am working on it right now.
szpiech
commented
11 years ago Cheers, I hope to be able to use it soon.
I have cloned into latest code that is posted here and compiled it. I'm looking to pass a frequency trajectory file. After running into plenty of exceptions, I decided to run a test simulation with -oTrace and then pass that trajectory back to msms.
java -jar msms.jar -N 10000 -ms 10 1 -t 4 -r 4 -SAA 5 -SAa 2.5 -SF 0 0.7 -Sp 0.5 -oTrace
I cut off all output that isn't related to the trajectory to get a frequency trace that looks like:
0.21575 0.9999 1.0E-4 0.215725 0.99985 1.5E-4 0.2157 0.99995 5.0E-5 0.215675 0.9999 1.0E-4 0.21565 0.9999 1.0E-4 0.215625 0.9998 2.0E-4 0.2156 0.99975 2.5E-4 0.21557500000000002 0.99975 2.5E-4 0.21555000000000002 0.99965 3.5E-4 0.21552500000000002 0.99965 3.5E-4 ...
Saving the complete trajectory in trajectory.txt and passing this to msms with -Strace gives the following error.
java -jar msms.jar -N 10000 -ms 10 1 -t 4 -r 4 -Strace trajectory.txt ms -N 10000 10 1 -t 4 -r 4 -Strace trajectory.txt [3.2rc Build:81] 0xb84cd0e908815ae3
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException at java.lang.System.arraycopy(Native Method) at at.mabs.model.selection.SuperFrequencyTrace.getFrequencys(SuperFrequencyTrace.java:142) at at.mabs.model.selection.SelectionData.getFrequency(SelectionData.java:268) at at.mabs.model.selection.SelectionData.coalescentCumulantIntegration(SelectionData.java:296) at at.mabs.coalescent.CoalescentEventCalculator.nextCoalescentSelection(CoalescentEventCalculator.java:361) at at.mabs.coalescent.CoalescentEventCalculator.nextEventSelection(CoalescentEventCalculator.java:90) at at.mabs.coalescent.CoalescentEventCalculator.calculateCoalescentHistory(CoalescentEventCalculator.java:520) at at.MSLike.run(MSLike.java:301) at at.MSLike.runThreads(MSLike.java:424) at at.MSLike.runMe(MSLike.java:191) at at.MSLike.main(MSLike.java:541) at at.MSLike.main(MSLike.java:585)
Somewhat perplexingly, about 10% of the time it "works" and produces output. For example:
java -jar msms.jar -N 10000 -ms 10 1 -t 4 -r 4 -Strace trajectory.txt ms -N 10000 10 1 -t 4 -r 4 -Strace trajectory.txt [3.2rc Build:81] 0xc5bc9fa71ec78045
// segsites: 6 positions: 0.0931092357 0.1244903960 0.2402095753 0.3468718393 0.7654496949 0.9065454944 010110 111110 010110 000000 110110 110110 110110 111110 010110 010111