-------Speciesnames:--------
species 0	monDom5
species 1	hg38
species 2	rheMac3
species 3	mm10
species 4	rn6
species 5	bosTau8
species 6	canFam3
species 7	galGal4
# assuming an SQLite database
read in the configuration file for extrinsic features
# Sources of extrinsic information: M RM E W 
# Setting acceptor splice site local malus: 0.1
# Setting donor splice site local malus: 0.1
# Setting exon local malus: 0.985
# Setting CDSpart local malus: 0.985
# Setting UTRpart local malus: 0.985
extrinsic group 1: none ... is deleted
extrinsic group 1: none ... is deleted
extrinsic group 1: monDom5 hg38 rheMac3 mm10 rn6 bosTau8 canFam3 galGal4
Trying to open database ../vertebrates.db
# human version. Using default transition matrix.
# setting temperature to 3 (for sampling)
number of nodes: 89
number of signatures=24. First 10 signatures are:
numAli	sumCumFragLen	sumAliLen	depth	color	signature
10	70389	19199	7     royalblue3         0:chr6+1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-
9	17566	6206	6      seagreen1                1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-
2	15742	7673	8         brown4 0:chr6+1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-7:chr14-
8	11321	4555	4  darkturquoise                                1:chr16+2:chr20+5:chr25+6:chr6-
4	6958	1777	7         grey40         0:chr6+1:chr16+2:chr20+3:chr17+4:chr10+5:chr25+6:chr6-
5	5831	2301	5        maroon2                         0:chr6+1:chr16+2:chr20+5:chr25+6:chr6-
5	4154	1875	6       skyblue4                 0:chr6+1:chr16+2:chr20+3:chr17-4:chr10-6:chr6-
4	2500	596	6     olivedrab1                1:chr16+2:chr20+3:chr17+4:chr10+5:chr25+6:chr6-
4	2009	655	5          khaki                        1:chr16+2:chr20+3:chr17-4:chr10-6:chr6-
1	1863	908	5         gray66                        1:chr16+3:chr17-4:chr10-5:chr25+6:chr6-
found 9 paths
Have 36 collisions.
aliG2 nodes 91 allPaths nodes 83 ratio: 0.912088
Have 0 collisions.
MILP objective=0
removing alignments 
0 geneRanges=alignments (0%) and 0 / 144705 = 0% of aligned bases and 0 / 312086 = 0% of aligment-range-covered bases were deleted because of too much redundancy.
findGeneRanges reduced the number of aligments from 1193 to 1 (to 0.0838%).
processing next gene range:
monDom5.chr6	+	0	59265
hg38.chr16	+	0	50999
rheMac3.chr20	+	0	55045
mm10.chr17	-	146501	178392
rn6.chr10	-	67330	99943
bosTau8.chr25	+	0	48694
canFam3.chr6	-	142212	184727
galGal4.chr14	-	148966	149998
Found 4653 ECs on species monDom5
Found 4601 ECs on species hg38
Found 4301 ECs on species rheMac3
Found 3030 ECs on species mm10
Found 2864 ECs on species rn6
Found 4663 ECs on species bosTau8
Found 3674 ECs on species canFam3
Found 123 ECs on species galGal4
OEs in this gene range must have at least 2 ECs
Found 1097 ortho exons
building Graph for monDom5
building Graph for hg38
building Graph for rheMac3
building Graph for mm10
building Graph for rn6
building Graph for bosTau8
building Graph for canFam3
building Graph for galGal4
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	-411.4732174	-207.168367	19
0	1	1	-366.4202182	-203.3242584	95
0	2	0.7071067812	-421.5244101	-215.5876463	25
0	3	0.7071067812	-296.2406438	-218.831819	27
0	4	0.7071067812	-343.7126381	-223.6217199	17
0	5	0.7071067812	-260.4884148	-223.6860823	30
0	6	0.7071067812	-264.6714384	-225.0250174	14
0	7	0.7071067812	-251.6136967	-227.2396537	3
0	8	0.7071067812	-244.3816518	-227.7231261	2
0	9	0.7071067812	-244.3816533	-228.3089141	2
0	10	0.7071067812	-244.3816533	-229.1373412	2
0	11	0.7071067812	-251.6136991	-229.6538696	5
0	12	0.7071067812	-238.5348944	-229.6478041	3
0	13	0.5773502692	-244.3816464	-230.1373343	2
0	14	0.5773502692	-238.5348917	-230.9406946	1
0	15	0.5773502692	-238.5348917	-231.0953952	1
0	16	0.5773502692	-238.5348882	-231.5180414	1
0	17	0.5773502692	-238.5348882	-231.672742	1
0	18	0.5773502692	-245.7669375	-231.8380564	4
0	19	0.5773502692	-238.5348917	-231.6727454	1
0	20	0.5	-238.5348917	-232.1727454	1
0	21	0.5	-232.2952659	-232.2952659	0
dual decomposition reduced initial duality gap of 179.1779515 to 0 (to 0%)
# total time: 112s
# command line:
# augustus --species=human --softmasking=1 --treefile=../tree.nwk --alnfile=1.maf --dbaccess=../vertebrates.db --speciesfilenames=../genomes.tbl --alternatives-from-evidence=0 --/CompPred/outdir=pred1
