-------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: hg38 mm10 rheMac3 galGal4
extrinsic group 2: none ... is deleted
extrinsic group 2: monDom5 rn6 bosTau8 canFam3
Trying to open database ../vertebrates_rnaseq.db
# human version. Using species specific transition matrix: /home/stefanie/augustus/trunks/config/species/human/human_trans_shadow_partial_utr.pbl
# setting temperature to 3 (for sampling)
number of nodes: 41
number of signatures=12. First 10 signatures are:
numAli	sumCumFragLen	sumAliLen	depth	color	signature
7	71598	28492	6     royalblue3                 0:chr6+1:chr16+2:chr20+5:chr25+6:chr6-7:chr14-
10	20966	9195	4      seagreen1                                1:chr16+2:chr20+5:chr25+6:chr6-
8	10080	5397	2         brown4                                               1:chr16+2:chr20+
1	6373	2218	5  darkturquoise                         0:chr6+1:chr16+2:chr20+5:chr25+6:chr6-
4	3319	1097	5         grey40                        1:chr16+2:chr20+5:chr25+6:chr6-7:chr14-
1	3194	1661	5        maroon2                         0:chr6+1:chr16+2:chr20+6:chr6-7:chr14-
1	1739	916	3       skyblue4                                        1:chr16+2:chr20+6:chr6-
2	1229	227	8     olivedrab1 0:chr6+1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-7:chr14-
2	880	410	4          khaki                               1:chr16+2:chr20+5:chr25+7:chr14-
2	649	230	3         gray66                                       1:chr16+2:chr20+5:chr25+
found 4 paths
Have 6 collisions.
aliG2 nodes 43 allPaths nodes 41 ratio: 0.953488
Have 0 collisions.
MILP objective=0
removing alignments 
0 geneRanges=alignments (0%) and 0 / 120130 = 0% of aligned bases and 0 / 421880 = 0% of aligment-range-covered bases were deleted because of too much redundancy.
findGeneRanges reduced the number of aligments from 734 to 1 (to 0.136%).
processing next gene range:
monDom5.chr6	+	249222	418977
hg38.chr16	+	99000	150999
rheMac3.chr20	+	109998	166549
mm10.chr17	-	28835	31713
rn6.chr10	-	35617	38480
bosTau8.chr25	+	87467	114938
canFam3.chr6	-	42755	93096
galGal4.chr14	-	48694	124708
# Delete group HintGroup , 19657-23313, mult= 2, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 30 groups.
# Deleted 1 groups because some hint was not satisfiable.
# Delete group HintGroup , 8745-9082, mult= 1, priority= 4 1 features
# Delete group HintGroup , 12847-15729, mult= 1, priority= 4 1 features
# Delete group HintGroup , 14979-17557, mult= 1, priority= 4 1 features
# Delete group HintGroup , 33778-33881, mult= 1, priority= 4 1 features
# Delete group HintGroup , 34035-34245, mult= 28, priority= 4 1 features
# Delete group HintGroup , 41099-41382, mult= 1, priority= 4 1 features
# Delete group HintGroup , 41378-41419, mult= 1, priority= 4 1 features
# Delete group HintGroup , 43315-43353, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 46 groups.
# Deleted 8 groups because some hint was not satisfiable.
# Delete group HintGroup , 2414-2465, mult= 1, priority= 4 1 features
# Delete group HintGroup , 2426-2566, mult= 1, priority= 4 1 features
# Delete group HintGroup , 9278-29589, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 20 groups.
# Deleted 3 groups because some hint was not satisfiable.
Found 13652 ECs on species monDom5
Found 5442 ECs on species hg38
Found 5145 ECs on species rheMac3
Found 366 ECs on species mm10
Found 210 ECs on species rn6
Found 2619 ECs on species bosTau8
Found 4447 ECs on species canFam3
Found 7747 ECs on species galGal4
OEs in this gene range must have at least 2 ECs
Found 1379 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	-402.0555943	-216.0151452	16
0	1	1	-371.9090378	-212.0292748	79
0	2	0.7071067812	-289.7389224	-221.3138191	12
0	3	0.7071067812	-272.6552973	-223.5761283	12
0	4	0.7071067812	-261.0435524	-223.1860786	9
0	5	0.5773502692	-249.0550221	-225.368991	4
0	6	0.5773502692	-261.4274989	-225.2353155	5
0	7	0.5	-237.4696317	-225.7813167	3
0	8	0.5	-226.3547191	-225.9071253	2
0	9	0.5	-237.4696317	-226.2813167	1
0	10	0.5	-226.3547191	-226.3547191	0
dual decomposition reduced initial duality gap of 175.7008753 to 0 (to 0%)
# total time: 144s
# command line:
# augustus --species=human --softmasking=1 --treefile=../tree.nwk --alnfile=2.maf --dbaccess=../vertebrates_rnaseq.db --speciesfilenames=../genomes.tbl --alternatives-from-evidence=0 --dbhints=1 --UTR=1 --allow_hinted_splicesites=atac --extrinsicCfgFile=../extrinsic-rnaseq.cfg --/CompPred/outdir=pred2
