-------Speciesnames:--------
species 0	hg19
species 1	mm9
species 2	bosTau4
species 3	galGal3
reading in file names for species from genomes.tbl
reading in bosTau4.chr1
reading in galGal3.chr1
reading in hg19.chr21
reading in mm9.chr16
# No extrinsic information given.
Running prediction...
# human version. Using default transition matrix.
# setting temperature to 3 (for sampling)
number of nodes: 1
number of signatures=0. First 10 signatures are:
numAli	sumCumFragLen	sumAliLen	depth	color	signature
found 0 paths
Have 0 collisions.
MILP objective=0
removing alignments
0 geneRanges=alignments (0%) and 0 / 58758 = 0% of aligned bases and 0 / 106809 = 0% of aligment-range-covered bases were deleted because of too much redundancy.
findGeneRanges reduced the number of aligments from 313 to 1 (to 0.319%).
processing gene range number 1
hg19.chr21	+	0	32084
mm9.chr16	+	0	25967
bosTau4.chr1	+	0	30874
galGal3.chr1	+	0	22282
Found 2566 ECs on species hg19
Found 2217 ECs on species mm9
Found 2643 ECs on species bosTau4
Found 2088 ECs on species galGal3
OEs in this gene range must have at least 2 ECs
Found 141 ortho exons
building Graph for hg19
building Graph for mm9
building Graph for bosTau4
building Graph for galGal3
computing omega for each ortho exon.
--- processing ortho exons on forward strand ---
generating codon alignment
Merge processing: Traverse alignment left to right
--- processing ortho exons on reverse strand ---
generating codon alignment
Merge processing: Traverse alignment left to right
compute omegas done
dual decomposition on gene Range 1
round	iter	step_size	primal	dual	#inconsistencies
0	0	0	96.42318205	137.9112869	4
0	1	10.37202622	127.1016117	168.5897175	34
0	2	1.220238405	127.1016026	149.0658933	16
0	3	1.372767597	127.1016041	127.1016136	16
0	4	1.192093046e-07	127.1016017	127.1016093	16
dual decomposition reduced initial duality gap of 30.67842727 to 0 (to 0%)
# command line:
# ../../bin/augustus --species=human --speciesfilenames=genomes.tbl --treefile=tree.nwk --alnfile=aln.maf --softmasking=0 --alternatives-from-evidence=0 --/CompPred/outdir=../../tests/examples/results/test_cgp/
