-------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: hg38
extrinsic group 2: monDom5 rheMac3 mm10 rn6 bosTau8 canFam3 galGal4
Trying to open database ../vertebrates_anno.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 4649 ECs on species monDom5
Found 4585 ECs on species hg38
Found 4296 ECs on species rheMac3
Found 3030 ECs on species mm10
Found 2862 ECs on species rn6
Found 4653 ECs on species bosTau8
Found 3675 ECs on species canFam3
Found 123 ECs on species galGal4
OEs in this gene range must have at least 2 ECs
Found 1088 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	23240.27933	23367.92025	13
0	1	1	23282.25944	23371.37537	88
0	2	0.7071067812	23194.61491	23362.24273	20
0	3	0.7071067812	23282.25825	23358.95997	32
0	4	0.7071067812	23193.19186	23354.02353	24
0	5	0.7071067812	23268.39726	23354.55261	42
0	6	0.5773502692	23291.77372	23350.76685	8
0	7	0.5773502692	23330.59914	23349.37898	5
0	8	0.5773502692	23325.57212	23348.24749	5
0	9	0.5773502692	23330.59913	23348.63849	2
0	10	0.5	23330.59913	23347.72428	2
0	11	0.5	23330.59913	23347.13849	2
0	12	0.5	23330.59913	23346.56958	2
0	13	0.5	23330.59913	23346.13849	2
0	14	0.5	23331.41887	23345.88365	6
0	15	0.5	23330.59913	23346.13849	2
0	16	0.4472135955	23330.59914	23345.24407	2
0	17	0.4472135955	23336.44589	23345.00671	1
0	18	0.4472135955	23336.44589	23344.76698	1
0	19	0.4472135955	23344.50026	23344.73998	2
0	20	0.4472135955	23336.44589	23344.76698	1
0	21	0.4082482905	23344.50026	23344.50026	0
dual decomposition reduced initial duality gap of 104.2209316 to 0 (to 0%)
# total time: 99s
# command line:
# augustus --species=human --softmasking=1 --treefile=../tree.nwk --alnfile=1.maf --dbaccess=../vertebrates_anno.db --speciesfilenames=../genomes.tbl --alternatives-from-evidence=0 --dbhints=1 --allow_hinted_splicesites=atac --extrinsicCfgFile=../extrinsic-anno.cfg --/CompPred/outdir=pred1
