RENTplus error

[Yan Wong]

This occasionally causes RENTplus to bomb out:

  File "/usr/lib/python3.4/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "./plots.py", line 739, in infer_worker
    """
  File "./plots.py", line 396, in run
    ret = self.__run_ARGweaver(skip_infer = metrics_only)
  File "./plots.py", line 506, in __run_RentPlus
    time = memory = None
  File "./plots.py", line 645, in run_rentplus
    cmd = ["java", "-jar", RentPlus_executable]
  File "./plots.py", line 329, in time_cmd
    raise ValueError(
ValueError: Error running 'java -jar /home/yan/treeseq-inference/src/../RentPlus/RentPlus.jar data/raw__NOBACKUP__/metrics_by_mutation_rate_with_demography/simulations/msprime-n15_NeGutenkunst.out.of.africa_l100000_rho0.00000001_mu0.00000376783-gs1640504192err0.001.dat': status=1:stderrb'Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -32768\n\tat java.util.ArrayList.elementData(ArrayList.java:418)\n\tat java.util.ArrayList.get(ArrayList.java:431)\n\tat main.Main.findCompatibleRegion(Main.java:660)\n\tat main.Main.makeGuideTrees(Main.java:466)\n\tat main.Main.<init>(Main.java:142)\n\tat main.Main.main(Main.java:2321)\nCommand exited with non-zero status 1\n119752 0.11 2.90\n'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "./plots.py", line 2876, in <module>
    if cls in classes:
  File "./plots.py", line 2870, in main
    try:
  File "./plots.py", line 2754, in run_infer
    class ProgramComparisonMemoryFigure(ProgramComparisonFigure):
  File "./plots.py", line 909, in infer
    
  File "/usr/lib/python3.4/multiprocessing/pool.py", line 689, in next
    raise value
ValueError: Error running 'java -jar /home/yan/treeseq-inference/src/../RentPlus/RentPlus.jar data/raw__NOBACKUP__/metrics_by_mutation_rate_with_demography/simulations/msprime-n15_NeGutenkunst.out.of.africa_l100000_rho0.00000001_mu0.00000376783-gs1640504192err0.001.dat': status=1:stderrb'Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -32768\n\tat java.util.ArrayList.elementData(ArrayList.java:418)\n\tat java.util.ArrayList.get(ArrayList.java:431)\n\tat main.Main.findCompatibleRegion(Main.java:660)\n\tat main.Main.makeGuideTrees(Main.java:466)\n\tat main.Main.<init>(Main.java:142)\n\tat main.Main.main(Main.java:2321)\nCommand exited with non-zero status 1\n119752 0.11 2.90\n'

[Jerome Kelleher]

java.lang.ArrayIndexOutOfBoundsException: -32768\

Nice. Looks like an overflow of a signed 16 bit int.

There's nothing we can do here except try and catch this error and just leave the corresponding entry in the stats tables as missing data.

[Yan Wong]

Now reported at SajadMirzaei/RentPlus#5