Hi,

I've come up with this SEGFAULT error:

./HYPHYMP TemplateBatchFiles/TestBranchDNDS.bf <
/home/avb/wallace/prokarya_archaea/pyrococcales/four_concat/options.TestBranchDN
DS.3.txt

I have grouped the necessary data/tree/options files to reproduce the bug in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login


Running HYPHYDebug in gdb I get:

Program received signal SIGSEGV, Segmentation fault.
0x080b8bb5 in _TheTree::ThreadReleafTreeCache (this=0x8799a48, dsf=0x8389278, index=10401, lastIndex=10400,
    startLeaf=0, endLeaf=3, position=657344, offset=0) at calcnode.cpp:7783
7783                                    *(fastIndex++) = *(nodeProbs++);

(gdb) backtrace
#0  0x080b8bb5 in _TheTree::ThreadReleafTreeCache (this=0x8799a48, dsf=0x8389278, index=10401,
    lastIndex=10400, startLeaf=0, endLeaf=3, position=657344, offset=0) at calcnode.cpp:7783
#1  0x080ff751 in _LikelihoodFunction::ComputeBlock (this=0x879b230, index=0, siteRes=0xa34e27f8)
    at likefunc.cpp:7943
#2  0x080eb0bf in _LikelihoodFunction::RecurseCategory (this=0x879b230, blockIndex=0, index=1, dependance=3,
    highestIndex=1, weight=0.071428571429688406) at likefunc.cpp:2375
#3  0x080eaf35 in _LikelihoodFunction::RecurseCategory (this=0x879b230, blockIndex=0, index=0, dependance=3,
    highestIndex=1, weight=1) at likefunc.cpp:2345
#4  0x080e9dae in _LikelihoodFunction::Compute (this=0x879b230) at likefunc.cpp:2037
#5  0x080f8efa in _LikelihoodFunction::ConjugateGradientDescent (this=0x879b230,
    precision=0.050000000000000003, bestVal=@0xbfffb8a0) at likefunc.cpp:5667
#6  0x080f1dda in _LikelihoodFunction:ptimize (this=0x879b230) at likefunc.cpp:3828
#7  0x08077a22 in _ElementaryCommand::Execute (this=0x822d848, chain=@0xbfffe520) at batchlan.cpp:6061
#8  0x080571d7 in _ExecutionList::Execute (this=0xbfffe520) at batchlan.cpp:1092
#9  0x0811c40b in main (argc=2, argv=0xbffff634) at main-unix.cp:779


This is happening with options:

(3):Both synonymous and non-synonymous rate varies across sites via two independent gamma/beta distributions.

How many rate classes should be ([3-8] is a good range, must be >=2)
8

If I use:

(1):No site-by-site rate variation.

I don't get this error.

Please tell me if I can add anymore info,

Bests,

    Albert.