segfault in augustus CGP 3.3.1

[MarioStanke]

Joel Armstrong sent this example via email on July 12, 2018:

augustus --dbhints=1 --allow_hinted_splicesites=atac
--extrinsicCfgFile=augustus-cgp-3.3.1-segfault/tmpXeNqPA.tmp
--species=human --treefile=augustus-cgp-3.3.1-segfault/tmp5wgnqb.tmp
--alnfile=augustus-cgp-3.3.1-segfault/tmpBWvb4O.tmp
--dbaccess=augustus-cgp-3.3.1-segfault/tmp9Ptygk.tmp
--speciesfilenames=augustus-cgp-3.3.1-segfault/yarrow-vm.31530.5456091091.tmp
--softmasking=1 --exoncands=1 --alternatives-from-evidence=0
--/CompPred/logreg=on --printOEs=1
--/CompPred/outdir=augustus-cgp-3.3.1-segfault

Found 3633 ortho exons
building Graph for monDom5
adding sampled states and additional exon candidates

augustus: ERROR
in SpeciesGraph::getPredTypes()
Segmentation fault (core dumped)

Debug output:

Breakpoint 1, SpeciesGraph::getPredType (this=0x5555570c10c0, type=intron_type, begin=1213, end=1510) at speciesgraph.cc:551
551 NodeType SpeciesGraph::getPredType(StateType type, int begin, int end){
(gdb) bt
#0 SpeciesGraph::getPredType (this=0x5555570c10c0, type=intron_type, begin=1213, end=1510) at speciesgraph.cc:551
#1 0x00005555557419bd in SpeciesGraph::addLeftSS (this=0x5555570c10c0, exon=0x55557415b4c0,
neutralLines=std::vector of length 15, capacity 16 = {...}, auxiliaryNodes=std::unordered_map with 0 elements) at speciesgraph.cc:447
#2 0x00005555557403b0 in SpeciesGraph::buildGraph (this=0x5555570c10c0, meanIntrLen=6910.7404295710676) at speciesgraph.cc:91
#3 0x0000555555716941 in CompGenePred::start (this=0x7fffffffd940) at compgenepred.cc:520
#4 0x0000555555567906 in main (argc=15, argv=0x7fffffffe198) at augustus.cc:129
(gdb) p type
$1 = intron_type
(gdb) up
#1 0x00005555557419bd in SpeciesGraph::addLeftSS (this=0x5555570c10c0, exon=0x55557415b4c0,
neutralLines=std::vector of length 15, capacity 16 = {...}, auxiliaryNodes=std::unordered_map with 0 elements) at speciesgraph.cc:447
447 NodeType ntype = getPredType(((State*)exon->item)->type, exon->begin, exon->end);
(gdb) l
442
443 Node* SpeciesGraph::addLeftSS(Status exon, vector< vector<Node> >&neutralLines, unordered_map<int32_t,Node*> &auxiliaryNodes){
444
445 if(!exon)
446 return NULL;
447 NodeType ntype = getPredType(((State*)exon->item)->type, exon->begin, exon->end);
448 int begin = exon->begin;
449 return addAuxilaryNode(ntype,begin,neutralLines, auxiliaryNodes);
450 }
451
(gdb) p exon
$2 = (Status *) 0x55557415b4c0
(gdb) p exon->item
$3 = (const void *) 0x555577c6b1e0
(gdb) p *(State *)exon->item
$5 = {begin = 1213, end = 1510, next = 0x555577c6b2d0, type = intron_type, prob = {static dbl_inf = inf, static max_val = 3.2733906078961419e+150,
static min_val = 3.0549363634996047e-151, static base = 1.0715086071862673e+301, static baseinv = 9.3326361850321888e-302,
static logbase = 693.14718055994535, static max_exponent = 2147483647, static min_exponent = -2147483648, static temperature = 0,
static rest = {4.2535295865117308e+37, 1.8092513943330656e+75, 7.6957043352332967e+112, 3.2733906078961419e+150, 1.3923463798895859e+188,
5.9223865215328557e+225, 2.5191046292098296e+263}, static output_precision = 3, value = 0, exponent = 0}, hasScore = true, apostprob = 1,
sampleCount = 11, evidence = 0x0, truncated = 0 '\000', framemod = 0}