-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_144

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.106725_t
Valid prediction for snap_scaffold_144-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_61380-T1
Valid prediction for Augustus_model.g40825.t1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_144-snap.1-T1
Couldn't classify 1567, 1605
Sorry, prediction GeneMark_model.106726_t fails validation.
(CAG)	 AG	1567-1605	GT	AGG
(TTA)	 AG	1710-1833	GT	AGG
(ACA)	 AG	1962-2065	GT	CTG
(CAA)	 AG	2170-2204	GT	AGG
(GTT)	 AG	2495-2653	GT	AGG
(GAG)	 AG	3209-3221	GC	AAG
-recovered GeneMark_model.106726_t, terminal, 3209, 3221
-recovered GeneMark_model.106726_t, internal, 1567, 1605
-recovered GeneMark_model.106726_t, internal, 1710, 1833
-recovered GeneMark_model.106726_t, internal, 1962, 2065
-recovered GeneMark_model.106726_t, internal, 2170, 2204
-recovered GeneMark_model.106726_t, internal, 2495, 2653
-recovered GeneMark_model.106726_t, internal, 3209, 3221
Valid prediction for snap_scaffold_144-snap.3-T1
Couldn't classify 11653, 11748
Sorry, prediction Augustus_model.g40824.t1 fails validation.
(ATG)	 GT	9632-9674	GT	AGG
(ACG)	 AG	10273-10368	GT	AGG
(TAT)	 AG	10472-10600	GT	AGG
(CTC)	 AG	10713-10937	GT	TGG
(CTC)	 AG	11188-11496	GT	AGG
(CAG)	 AG	11653-11748	GT	AAG
-recovered Augustus_model.g40824.t1, initial, 9632, 9674
-recovered Augustus_model.g40824.t1, internal, 10273, 10368
-recovered Augustus_model.g40824.t1, internal, 10472, 10600
-recovered Augustus_model.g40824.t1, internal, 10713, 10937
-recovered Augustus_model.g40824.t1, internal, 11188, 11496
-recovered Augustus_model.g40824.t1, internal, 11653, 11748
Couldn't classify 1567, 1833
Sorry, prediction GlimmerHMM_glimmerT_61381-T1 fails validation.
(CAG)	 AG	1567-1833	GT	AGG
(CTC)	 AG	1944-2204	GT	AGG
(CTC)	 AG	2401-2732	AG	AAA
-recovered GlimmerHMM_glimmerT_61381-T1, terminal, 2401, 2732
-recovered GlimmerHMM_glimmerT_61381-T1, internal, 1567, 1833
-recovered GlimmerHMM_glimmerT_61381-T1, internal, 1944, 2204
Couldn't classify 11282, 11443
Sorry, prediction GeneMark_model.106724_t fails validation.
(ATG)	 GT	9632-9674	GT	AGG
(GCG)	 AG	10333-10368	GT	AGG
(TAT)	 AG	10472-10600	GT	AGG
(GAG)	 AG	10769-10844	GT	TTG
(GTT)	 AG	11282-11443	GT	AGG
-recovered GeneMark_model.106724_t, initial, 9632, 9674
-recovered GeneMark_model.106724_t, internal, 10333, 10368
-recovered GeneMark_model.106724_t, internal, 10472, 10600
-recovered GeneMark_model.106724_t, internal, 10769, 10844
-recovered GeneMark_model.106724_t, internal, 11282, 11443
Valid prediction for GlimmerHMM_glimmerT_61379-T1
Couldn't classify 11187, 11496
Couldn't classify 11653, 11723
Sorry, prediction pasa_asmbl_13862.p1 fails validation.
(GCT)	 CA	11187-11496	GT	AGG
(CAG)	 AG	11653-11723	GT	TGG
-recovered pasa_asmbl_13862.p1, internal, 11653, 11723
Couldn't classify 1725, 1833
Sorry, prediction pasa_asmbl_13866.p1 fails validation.
(GCA)	 AC	1725-1833	GT	AGG
(CTC)	 AG	1944-2204	GT	AGG
(CTC)	 AG	2401-2706	GT	AGG
(AAG)	 AG	2879-2965	GT	AAG
(GAG)	 AG	3082-3185	AT	AGA
-recovered pasa_asmbl_13866.p1, terminal, 3082, 3185
-recovered pasa_asmbl_13866.p1, internal, 1944, 2204
-recovered pasa_asmbl_13866.p1, internal, 2401, 2706
-recovered pasa_asmbl_13866.p1, internal, 2879, 2965
Valid prediction for Augustus_model.g40826.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 12646
-exon list size: 63


building trellis

1.5    
3.1    
4.6    
6.2    
7.7    
9.2    
10.8    
12.3    
13.8    
15.4    
16.9    
18.5    
20.0    
21.5    
23.1    
24.6    
26.2    
27.7    
29.2    
30.8    
32.3    
33.8    
35.4    
36.9    
38.5    
40.0    
41.5    
43.1    
44.6    
46.2    
47.7    
49.2    
50.8    
52.3    
53.8    
55.4    
56.9    
58.5    
60.0    
61.5    
63.1    
64.6    
66.2    
67.7    
69.2    
70.8    
72.3    
73.8    
75.4    
76.9    
78.5    
80.0    
81.5    
83.1    
84.6    
86.2    
87.7    
89.2    
90.8    
92.3    
93.8    
95.4    
96.9    
98.5    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support