-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_18326624-18486637

-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 GlimmerHMM_glimmerT_23854-T1
Valid prediction for Augustus_model.g15875.t1
Valid prediction for snap_scaffold_9-snap.3671-T1
Valid prediction for snap_scaffold_9-snap.3637-T1
Valid prediction for GlimmerHMM_glimmerT_23860-T1
Valid prediction for GlimmerHMM_glimmerT_23857-T1
Valid prediction for snap_scaffold_9-snap.3670-T1
Valid prediction for GlimmerHMM_glimmerT_23851-T1
Valid prediction for GlimmerHMM_glimmerT_23867-T1
Couldn't classify 63066, 63089
Sorry, prediction pasa_asmbl_54665.p1 fails validation.
(CAT)	 TG	63066-63089	GT	TAG
(GAC)	 AG	63510-63652	GT	AGG
(ATG)	 AG	63878-64075	GT	TGG
(TGT)	 AG	64267-64384	AA	AAA
-recovered pasa_asmbl_54665.p1, initial, 63878, 64075
-recovered pasa_asmbl_54665.p1, terminal, 64267, 64384
-recovered pasa_asmbl_54665.p1, internal, 63510, 63652
-recovered pasa_asmbl_54665.p1, internal, 63878, 64075
Valid prediction for CodingQuarry_transcript_62474-T1
Valid prediction for Augustus_model.g15865.t1
Valid prediction for GlimmerHMM_glimmerT_23842-T1
Valid prediction for Augustus_model.g15882.t1
Valid prediction for Augustus_model.g15870.t1
Valid prediction for GlimmerHMM_glimmerT_23846-T1
Valid prediction for GlimmerHMM_glimmerT_23868-T1
Valid prediction for GlimmerHMM_glimmerT_23866-T1
Valid prediction for snap_scaffold_9-snap.3646-T1
Valid prediction for Augustus_model.g15879.t1
Valid prediction for Augustus_model.g15878.t1
Valid prediction for GlimmerHMM_glimmerT_23843-T1
Valid prediction for GlimmerHMM_glimmerT_23839-T1
Valid prediction for GlimmerHMM_glimmerT_23848-T1
Valid prediction for GlimmerHMM_glimmerT_23845-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.3660-T1
Valid prediction for Augustus_model.g15868.t1
Valid prediction for GlimmerHMM_glimmerT_23856-T1
Valid prediction for snap_scaffold_9-snap.3647-T1
Valid prediction for snap_scaffold_9-snap.3642-T1
Valid prediction for snap_scaffold_9-snap.3640-T1
Valid prediction for Augustus_model.g15881.t1
Valid prediction for GlimmerHMM_glimmerT_23858-T1
Valid prediction for GlimmerHMM_glimmerT_23863-T1
Valid prediction for snap_scaffold_9-snap.3648-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23855-T1
Valid prediction for snap_scaffold_9-snap.3650-T1
Valid prediction for CodingQuarry_transcript_62473-T1
Valid prediction for snap_scaffold_9-snap.3649-T1
Valid prediction for snap_scaffold_9-snap.3666-T1
Valid prediction for Augustus_model.g15866.t1
Valid prediction for Augustus_model.g15874.t1
Valid prediction for snap_scaffold_9-snap.3667-T1
Valid prediction for snap_scaffold_9-snap.3669-T1
Valid prediction for GlimmerHMM_glimmerT_23850-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_9-snap.3639-T1
Valid prediction for snap_scaffold_9-snap.3641-T1
Valid prediction for snap_scaffold_9-snap.3653-T1
Valid prediction for Augustus_model.g15862.t1
Valid prediction for snap_scaffold_9-snap.3657-T1
Valid prediction for Augustus_model.g15877.t1
Couldn't classify 126748, 126957
Sorry, prediction pasa_asmbl_55699.p1 fails validation.
(ACA)	 CC	126748-126957	GT	AGG
(CTG)	 AG	128145-128198	GT	AGG
(GCA)	 AG	129262-129379	GT	AGG
(AAT)	 AG	130004-130130	GT	AAG
(AGA)	 AG	130611-130689	GT	GGG
(GCA)	 AG	130874-130956	GT	AAG
(GGC)	 AG	131250-131331	GA	AGG
-recovered pasa_asmbl_55699.p1, terminal, 131250, 131331
-recovered pasa_asmbl_55699.p1, internal, 128145, 128198
-recovered pasa_asmbl_55699.p1, internal, 129262, 129379
-recovered pasa_asmbl_55699.p1, internal, 130004, 130130
-recovered pasa_asmbl_55699.p1, internal, 130611, 130689
-recovered pasa_asmbl_55699.p1, internal, 130874, 130956
Valid prediction for GlimmerHMM_glimmerT_23847-T1
Valid prediction for snap_scaffold_9-snap.3643-T1
Valid prediction for snap_scaffold_9-snap.3654-T1
Valid prediction for snap_scaffold_9-snap.3656-T1
Valid prediction for GlimmerHMM_glimmerT_23849-T1
Valid prediction for Augustus_model.g15876.t1
Valid prediction for snap_scaffold_9-snap.3659-T1
Valid prediction for snap_scaffold_9-snap.3645-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.3662-T1
Valid prediction for GlimmerHMM_glimmerT_23862-T1
Valid prediction for snap_scaffold_9-snap.3664-T1
Valid prediction for Augustus_model.g15871.t1
Valid prediction for GlimmerHMM_glimmerT_23838-T1
Valid prediction for Augustus_model.g15867.t1
Valid prediction for CodingQuarry_transcript_62476-T1
Valid prediction for Augustus_model.g15873.t1
Valid prediction for Augustus_model.g15861.t1
Couldn't classify 91832, 92008
Sorry, prediction pasa_asmbl_55701.p1 fails validation.
(GCA)	 GG	91832-92008	GT	TGG
(ATG)	 AG	92190-92252	GT	AGG
(GTG)	 AG	92322-92417	GT	AGG
(GAT)	 AG	93714-93860	GA	GAG
-recovered pasa_asmbl_55701.p1, initial, 92190, 92252
-recovered pasa_asmbl_55701.p1, terminal, 93714, 93860
-recovered pasa_asmbl_55701.p1, internal, 92190, 92252
-recovered pasa_asmbl_55701.p1, internal, 92322, 92417
Valid prediction for GlimmerHMM_glimmerT_23844-T1
Valid prediction for GlimmerHMM_glimmerT_23865-T1
Valid prediction for snap_scaffold_9-snap.3663-T1
Couldn't classify 79094, 79139
Couldn't classify 80151, 80234
Sorry, prediction pasa_asmbl_55703.p1 fails validation.
(AAG)	 AG	79094-79139	GT	GGG
(ATT)	 AG	79245-79294	GT	AGG
(CAA)	 AG	79439-79492	GT	AGG
(AAC)	 AG	79618-79768	GT	AGG
(AGA)	 AG	79988-80070	GT	GTG
(ATC)	 AG	80151-80234	GT	AGG
-recovered pasa_asmbl_55703.p1, internal, 79094, 79139
-recovered pasa_asmbl_55703.p1, internal, 79245, 79294
-recovered pasa_asmbl_55703.p1, internal, 79439, 79492
-recovered pasa_asmbl_55703.p1, internal, 79618, 79768
-recovered pasa_asmbl_55703.p1, internal, 79988, 80070
-recovered pasa_asmbl_55703.p1, internal, 80151, 80234
Valid prediction for snap_scaffold_9-snap.3638-T1
Valid prediction for snap_scaffold_9-snap.3644-T1
Valid prediction for GlimmerHMM_glimmerT_23841-T1
Couldn't classify 86048, 86257
Couldn't classify 88529, 88608
Sorry, prediction pasa_asmbl_55702.p1 fails validation.
(CAG)	 TC	86048-86257	GT	AAG
(TTG)	 AG	86347-86628	GT	CGG
(GAT)	 AG	86785-87071	GT	AGG
(GAG)	 AG	88064-88140	GT	AGG
(AGA)	 AG	88529-88608	GT	AGG
-recovered pasa_asmbl_55702.p1, internal, 86347, 86628
-recovered pasa_asmbl_55702.p1, internal, 86785, 87071
-recovered pasa_asmbl_55702.p1, internal, 88064, 88140
-recovered pasa_asmbl_55702.p1, internal, 88529, 88608
Valid prediction for Augustus_model.g15863.t1
Valid prediction for GlimmerHMM_glimmerT_23853-T1
Valid prediction for CodingQuarry_transcript_62477-T1
Valid prediction for snap_scaffold_9-snap.3655-T1
Valid prediction for pasa_asmbl_55711.p1
Valid prediction for snap_scaffold_9-snap.3658-T1
Valid prediction for Augustus_model.g15860.t1
Valid prediction for GlimmerHMM_glimmerT_23859-T1
Valid prediction for snap_scaffold_9-snap.3652-T1
Valid prediction for GlimmerHMM_glimmerT_23837-T1
Valid prediction for Augustus_model.g15869.t1
Valid prediction for snap_scaffold_9-snap.3665-T1
Valid prediction for snap_scaffold_9-snap.3636-T1
Valid prediction for GlimmerHMM_glimmerT_23852-T1
Valid prediction for GlimmerHMM_glimmerT_23840-T1
Valid prediction for Augustus_model.g15880.t1
Valid prediction for GlimmerHMM_glimmerT_23864-T1
Valid prediction for snap_scaffold_9-snap.3672-T1
Valid prediction for Augustus_model.g15872.t1
Valid prediction for snap_scaffold_9-snap.3668-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g15864.t1
Couldn't classify 3418, 3843
Sorry, prediction pasa_asmbl_54669.p1 fails validation.
(CGC)	 TC	3418-3843	GG	ACG
Valid prediction for CodingQuarry_transcript_62480-T1
Valid prediction for CodingQuarry_transcript_62479-T1
Valid prediction for snap_scaffold_9-snap.3651-T1
Valid prediction for CodingQuarry_transcript_62475-T1
Valid prediction for GlimmerHMM_glimmerT_23861-T1
Valid prediction for snap_scaffold_9-snap.3661-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18793, rend_intergenic: 16145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24597, rend_intergenic: 20503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160014
-exon list size: 296


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.4    
6.7    
7.0    
7.4    
7.7    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.1    
11.4    
11.7    
12.1    
12.4    
12.8    
13.1    
13.4    
13.8    
14.1    
14.4    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.8    
17.1    
17.4    
17.8    
18.1    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.8    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.2    
27.5    
27.9    
28.2    
28.5    
28.9    
29.2    
29.5    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.6    
37.9    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.3    
42.6    
43.0    
43.3    
43.6    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
47.0    
47.3    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.7    
53.0    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.4    
56.7    
57.0    
57.4    
57.7    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.1    
62.4    
62.8    
63.1    
63.4    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.5    
70.8    
71.1    
71.5    
71.8    
72.1    
72.5    
72.8    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.2    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.9    
82.2    
82.6    
82.9    
83.2    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.6    
85.9    
86.2    
86.6    
86.9    
87.2    
87.6    
87.9    
88.3    
88.6    
88.9    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.3    
92.6    
93.0    
93.3    
93.6    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 18793, rend_intergenic: 16145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24597, rend_intergenic: 20503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support