-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_17911023-18033298

-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 snap_scaffold_3-snap.3517-T1
Valid prediction for snap_scaffold_3-snap.3515-T1
Valid prediction for GlimmerHMM_glimmerT_8286-T1
Valid prediction for GlimmerHMM_glimmerT_8285-T1
Valid prediction for GlimmerHMM_glimmerT_8283-T1
Valid prediction for snap_scaffold_3-snap.3514-T1
Valid prediction for snap_scaffold_3-snap.3499-T1
Valid prediction for GlimmerHMM_glimmerT_8288-T1
Valid prediction for GlimmerHMM_glimmerT_8274-T1
Valid prediction for Augustus_model.g5457.t1
Valid prediction for snap_scaffold_3-snap.3494-T1
Valid prediction for snap_scaffold_3-snap.3509-T1
Valid prediction for snap_scaffold_3-snap.3503-T1
Couldn't classify 118013, 118057
Couldn't classify 119316, 119381
Sorry, prediction pasa_asmbl_40721.p1 fails validation.
(AAT)	 CC	118013-118057	GT	AGG
(ACT)	 AG	118877-119065	GT	AGG
(GCG)	 AG	119316-119381	CC	ATC
-recovered pasa_asmbl_40721.p1, internal, 118877, 119065
Valid prediction for snap_scaffold_3-snap.3498-T1
Couldn't classify 97298, 98800
Sorry, prediction pasa_asmbl_40719.p1 fails validation.
(GCC)	 AC	97298-98800	AA	TCA
Valid prediction for snap_scaffold_3-snap.3496-T1
Valid prediction for GlimmerHMM_glimmerT_8276-T1
Valid prediction for GlimmerHMM_glimmerT_8273-T1
Valid prediction for snap_scaffold_3-snap.3510-T1
Valid prediction for Augustus_model.g5456.t1
Valid prediction for snap_scaffold_3-snap.3497-T1
Valid prediction for GlimmerHMM_glimmerT_8289-T1
Valid prediction for snap_scaffold_3-snap.3508-T1
Couldn't classify 109468, 109526
Couldn't classify 115253, 115487
Sorry, prediction pasa_asmbl_40720.p1 fails validation.
(AAA)	 AG	109468-109526	GT	AGG
(AAT)	 AG	109908-110012	GT	AGG
(CTT)	 AG	110700-110826	GT	AGG
(GAG)	 AG	112258-112395	GT	AGG
(CTC)	 AG	112479-112532	GT	AGG
(CTG)	 AG	112691-112920	GT	AAG
(GGA)	 AG	113221-113317	GT	GGG
(CTA)	 AG	113477-113600	GT	AGG
(AAG)	 AG	113989-114140	GT	AGG
(GAT)	 AG	114286-114637	GT	AGG
(ATG)	 AG	114837-114894	GT	GGG
(GGG)	 AG	114972-115043	GT	AGG
(GGG)	 AG	115253-115487	AC	ACA
-recovered pasa_asmbl_40720.p1, initial, 114837, 114894
-recovered pasa_asmbl_40720.p1, internal, 109468, 109526
-recovered pasa_asmbl_40720.p1, internal, 109908, 110012
-recovered pasa_asmbl_40720.p1, internal, 110700, 110826
-recovered pasa_asmbl_40720.p1, internal, 112258, 112395
-recovered pasa_asmbl_40720.p1, internal, 112479, 112532
-recovered pasa_asmbl_40720.p1, internal, 112691, 112920
-recovered pasa_asmbl_40720.p1, internal, 113221, 113317
-recovered pasa_asmbl_40720.p1, internal, 113477, 113600
-recovered pasa_asmbl_40720.p1, internal, 113989, 114140
-recovered pasa_asmbl_40720.p1, internal, 114286, 114637
-recovered pasa_asmbl_40720.p1, internal, 114837, 114894
-recovered pasa_asmbl_40720.p1, internal, 114972, 115043
Valid prediction for snap_scaffold_3-snap.3511-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_3-snap.3504-T1
Valid prediction for GlimmerHMM_glimmerT_8284-T1
Valid prediction for snap_scaffold_3-snap.3506-T1
Valid prediction for snap_scaffold_3-snap.3505-T1
Valid prediction for Augustus_model.g5452.t1
Valid prediction for snap_scaffold_3-snap.3518-T1
Valid prediction for CodingQuarry_transcript_46463-T1
Valid prediction for snap_scaffold_3-snap.3519-T1
Valid prediction for snap_scaffold_3-snap.3512-T1
Valid prediction for Augustus_model.g5454.t1
Valid prediction for GlimmerHMM_glimmerT_8282-T1
Valid prediction for snap_scaffold_3-snap.3502-T1
Valid prediction for GlimmerHMM_glimmerT_8278-T1
Valid prediction for GlimmerHMM_glimmerT_8281-T1
Valid prediction for snap_scaffold_3-snap.3516-T1
Valid prediction for snap_scaffold_3-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_8277-T1
Valid prediction for snap_scaffold_3-snap.3520-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g5451.t1
Valid prediction for GlimmerHMM_glimmerT_8280-T1
Couldn't classify 64621, 64658
Couldn't classify 66400, 66419
Sorry, prediction pasa_asmbl_39584.p1 fails validation.
(GTT)	 GT	64621-64658	GT	CAG
(CTG)	 AG	64924-65014	GT	AGG
(AAA)	 AG	65104-65154	GT	TGG
(GAC)	 AG	65399-65486	GT	AGG
(ACG)	 AG	65817-65881	GT	TGG
(CGT)	 AG	65977-66031	GT	CAG
(TTG)	 AG	66400-66419	AG	CCA
-recovered pasa_asmbl_39584.p1, internal, 64924, 65014
-recovered pasa_asmbl_39584.p1, internal, 65104, 65154
-recovered pasa_asmbl_39584.p1, internal, 65399, 65486
-recovered pasa_asmbl_39584.p1, internal, 65817, 65881
-recovered pasa_asmbl_39584.p1, internal, 65977, 66031
Valid prediction for Augustus_model.g5455.t1
Valid prediction for Augustus_model.g5450.t1
Valid prediction for snap_scaffold_3-snap.3500-T1
Valid prediction for snap_scaffold_3-snap.3495-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8279-T1
Valid prediction for snap_scaffold_3-snap.3507-T1
Valid prediction for Augustus_model.g5449.t1
Valid prediction for snap_scaffold_3-snap.3501-T1
Valid prediction for Augustus_model.g5453.t1
Valid prediction for GlimmerHMM_glimmerT_8275-T1
Valid prediction for GlimmerHMM_glimmerT_8287-T1
Valid prediction for pasa_asmbl_39580.p1
Valid prediction for pasa_asmbl_39579.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 82890, rend_intergenic: 61682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86986, rend_intergenic: 85507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92956, rend_intergenic: 91360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119417, rend_intergenic: 106294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 122276
-exon list size: 255


building trellis

0.4    
0.8    
1.2    
1.6    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.4    
5.8    
6.2    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
8.9    
9.3    
9.7    
10.1    
10.5    
10.9    
11.3    
11.7    
12.1    
12.5    
12.8    
13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.7    
19.1    
19.5    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.8    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.2    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.7    
38.1    
38.5    
38.9    
39.3    
39.7    
40.1    
40.5    
40.9    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.9    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.1    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.1    
59.5    
59.9    
60.3    
60.7    
61.1    
61.5    
61.9    
62.3    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.8    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.5    
80.9    
81.3    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.7    
89.1    
89.5    
89.9    
90.3    
90.7    
91.1    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.8    
94.2    
94.6    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.4    
98.8    
99.2    
99.6    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 82890, rend_intergenic: 61682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86986, rend_intergenic: 85507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92956, rend_intergenic: 91360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119417, rend_intergenic: 106294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support