-------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/mario/augustus/git/Augustus/config/species/human/human_trans_shadow_partial_utr.pbl
# setting temperature to 3 (for sampling)
number of nodes: 93
number of signatures=26. First 10 signatures are:
numAli	sumCumFragLen	sumAliLen	depth	color	signature
9	82688	15379	8     royalblue3 0:chr6+1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-7:chr14-
14	34335	9661	6      seagreen1                1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-
4	34324	10672	7         brown4         0:chr6+1:chr16+2:chr20+3:chr17-5:chr25+6:chr6-7:chr14-
4	20979	6036	6  darkturquoise                 0:chr6+1:chr16+2:chr20+3:chr17-5:chr25+6:chr6-
2	4491	1673	5         grey40                        1:chr16+3:chr17-4:chr10-5:chr25+6:chr6-
3	4128	1009	5        maroon2                        1:chr16+2:chr20+3:chr17-5:chr25+6:chr6-
9	3451	1089	4       skyblue4                                1:chr16+2:chr20+5:chr25+6:chr6-
4	1827	386	7     olivedrab1        1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+6:chr6-7:chr14-
3	1726	581	5          khaki                        1:chr16+2:chr20+5:chr25+6:chr6-7:chr14-
5	1590	396	5         gray66                       1:chr16+2:chr20+3:chr17-4:chr10-5:chr25+
found 4 paths
Have 2 collisions.
aliG2 nodes 95 allPaths nodes 93 ratio: 0.978947
Have 0 collisions.
MILP objective=0
removing alignments 
0 geneRanges=alignments (0%) and 0 / 193477 = 0% of aligned bases and 0 / 440021 = 0% of aligment-range-covered bases were deleted because of too much redundancy.
findGeneRanges reduced the number of aligments from 1727 to 1 (to 0.0579%).
processing next gene range:
monDom5.chr6	+	411136	540518
hg38.chr16	+	149013	200999
rheMac3.chr20	+	165999	214434
mm10.chr17	-	0	61394
rn6.chr10	-	7884	38506
bosTau8.chr25	+	112924	153145
canFam3.chr6	-	4341	44769
galGal4.chr14	-	0	52426
# Delete group HintGroup , 32418-32644, mult= 1, priority= 4 1 features
# Delete group HintGroup , 38914-39154, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 46 groups.
# Deleted 2 groups because some hint was not satisfiable.
# Delete group HintGroup , 35563-35703, mult= 1, priority= 4 1 features
# Error: intron hint is too short.
# chr20	b2h	intron	41148	41184	0	.	.	mult=6;pri=4;src=E "60086.4;0.34;0:0"
# Delete group HintGroup , 41147-41183, mult= 6, priority= 4 1 features
# Delete group HintGroup , 45494-46260, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 41 groups.
# Deleted 3 groups because some hint was not satisfiable.
# Delete group HintGroup , 42523-42577, mult= 1, priority= 4 1 features
# Delete group HintGroup , 42631-55308, mult= 1, priority= 4 1 features
# Delete group HintGroup , 43586-43638, mult= 2, priority= 4 1 features
# Delete group HintGroup , 45693-45781, mult= 1, priority= 4 1 features
# Delete group HintGroup , 45774-45870, mult= 74, priority= 4 1 features
# Delete group HintGroup , 45905-46885, mult= 2, priority= 4 1 features
# Delete group HintGroup , 46851-47210, mult= 1, priority= 4 1 features
# Delete group HintGroup , 46854-47196, mult= 1, priority= 4 1 features
# Delete group HintGroup , 46915-47400, mult= 1, priority= 4 1 features
# Delete group HintGroup , 48467-48882, mult= 1, priority= 4 1 features
# Delete group HintGroup , 49470-49530, mult= 1, priority= 4 1 features
# Delete group HintGroup , 52574-52633, mult= 1, priority= 4 1 features
# Delete group HintGroup , 52778-52847, mult= 1, priority= 4 1 features
# Delete group HintGroup , 52791-52965, mult= 2, priority= 4 1 features
# Delete group HintGroup , 52819-52947, mult= 1, priority= 4 1 features
# Forced unstranded hint group to the only possible strand for 121 groups.
# Deleted 15 groups because some hint was not satisfiable.
# Forced unstranded hint group to the only possible strand for 15 groups.
Found 10221 ECs on species monDom5
Found 6112 ECs on species hg38
Found 5881 ECs on species rheMac3
Found 6210 ECs on species mm10
Found 2917 ECs on species rn6
Found 4613 ECs on species bosTau8
Found 3829 ECs on species canFam3
Found 5578 ECs on species galGal4
OEs in this gene range must have at least 2 ECs
Found 2009 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	-212.1208235	48.01202201	26
0	1	10.00510944	-74.00132569	232.8294716	192
0	2	1.598077069	-76.30996473	91.03697418	59
0	3	2.79725932	-63.17602956	11.59806036	20
0	4	3.738704496	-143.5904525	22.49239658	22
0	5	3.89401937	-58.33001179	20.71567105	25
0	6	3.161827314	-20.09459387	3.948670852	15
0	7	1.602884315	-34.94783332	5.372343051	10
0	8	2.546693692	-3.549327863	7.081572997	13
0	9	0.8177616046	-48.31512072	0.468818831	7
0	10	0.5740209562	-45.34296849	-2.647583914	4
0	11	0.2254359871	-30.25683759	-3.142843706	2
0	12	0.2032420784	-3.549317596	-3.549317596	0
dual decomposition reduced initial duality gap of 208.5715059 to 0 (to 0%)
# total time: 302s
# command line:
# augustus --species=human --softmasking=1 --treefile=../tree.nwk --alnfile=4.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=pred4
