-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_4713953-4865939

-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_55589-T1
Valid prediction for GlimmerHMM_glimmerT_55580-T1
Valid prediction for GlimmerHMM_glimmerT_55587-T1
Valid prediction for snap_scaffold_26-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_55569-T1
Valid prediction for GlimmerHMM_glimmerT_55577-T1
Valid prediction for Augustus_model.g36808.t1
Couldn't classify 70595, 70618
Couldn't classify 73569, 73886
Sorry, prediction pasa_asmbl_34925.p2 fails validation.
(GAC)	 TG	70595-70618	GT	AGG
(GTT)	 AG	71777-71968	GT	AGG
(GAG)	 AG	73569-73886	AA	AGA
-recovered pasa_asmbl_34925.p2, internal, 71777, 71968
Couldn't classify 114076, 114178
Sorry, prediction pasa_asmbl_34932.p1 fails validation.
(GGC)	 TA	114076-114178	GT	AGG
(AGT)	 AG	114271-114320	GT	AGG
(ATT)	 AG	117269-117312	GT	AGG
(GTC)	 AG	117921-118041	GT	AGG
(GCC)	 AG	118615-118713	GT	AGG
(GAG)	 AG	120594-120740	GT	GAG
-recovered pasa_asmbl_34932.p1, terminal, 120594, 120740
-recovered pasa_asmbl_34932.p1, internal, 114271, 114320
-recovered pasa_asmbl_34932.p1, internal, 117269, 117312
-recovered pasa_asmbl_34932.p1, internal, 117921, 118041
-recovered pasa_asmbl_34932.p1, internal, 118615, 118713
-recovered pasa_asmbl_34932.p1, internal, 120594, 120740
Valid prediction for snap_scaffold_26-snap.1052-T1
Valid prediction for snap_scaffold_26-snap.1038-T1
Valid prediction for snap_scaffold_26-snap.1026-T1
Valid prediction for snap_scaffold_26-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_55578-T1
Valid prediction for snap_scaffold_26-snap.1029-T1
Valid prediction for snap_scaffold_26-snap.1040-T1
Valid prediction for snap_scaffold_26-snap.1034-T1
Valid prediction for GlimmerHMM_glimmerT_55582-T1
Couldn't classify 74037, 74747
Sorry, prediction pasa_asmbl_34926.p1 fails validation.
(GGG)	 AC	74037-74747	TA	AAT
Valid prediction for snap_scaffold_26-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_55575-T1
Valid prediction for Augustus_model.g36815.t1
Valid prediction for Augustus_model.g36810.t1
Valid prediction for Augustus_model.g36820.t1
Valid prediction for Augustus_model.g36814.t1
Valid prediction for snap_scaffold_26-snap.1033-T1
Valid prediction for snap_scaffold_26-snap.1031-T1
Valid prediction for Augustus_model.g36807.t1
Valid prediction for Augustus_model.g36812.t1
Couldn't classify 108657, 108712
Sorry, prediction pasa_asmbl_34930.p1 fails validation.
(ATG)	 AT	105540-105607	GT	AGG
(GGC)	 AG	105768-105919	GT	AGG
(ACG)	 AG	106090-106195	GT	AGG
(GTT)	 AG	107143-107191	GT	GGG
(CTT)	 AG	107991-108027	GT	AGG
(GAA)	 AG	108657-108712	GG	CAG
-recovered pasa_asmbl_34930.p1, initial, 105540, 105607
-recovered pasa_asmbl_34930.p1, terminal, 105768, 105919
-recovered pasa_asmbl_34930.p1, internal, 105768, 105919
-recovered pasa_asmbl_34930.p1, internal, 106090, 106195
-recovered pasa_asmbl_34930.p1, internal, 107143, 107191
-recovered pasa_asmbl_34930.p1, internal, 107991, 108027
Valid prediction for snap_scaffold_26-snap.1037-T1
Valid prediction for Augustus_model.g36806.t1
Valid prediction for GlimmerHMM_glimmerT_55586-T1
Valid prediction for snap_scaffold_26-snap.1025-T1
Valid prediction for snap_scaffold_26-snap.1047-T1
Valid prediction for Augustus_model.g36813.t1
Valid prediction for snap_scaffold_26-snap.1046-T1
Valid prediction for Augustus_model.g36816.t1
Valid prediction for GlimmerHMM_glimmerT_55573-T1
Valid prediction for snap_scaffold_26-snap.1044-T1
Valid prediction for Augustus_model.g36821.t1
Valid prediction for snap_scaffold_26-snap.1043-T1
Valid prediction for snap_scaffold_26-snap.1056-T1
Valid prediction for snap_scaffold_26-snap.1059-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_26-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_55576-T1
Valid prediction for GlimmerHMM_glimmerT_55590-T1
Valid prediction for GlimmerHMM_glimmerT_55574-T1
Valid prediction for GlimmerHMM_glimmerT_55571-T1
Valid prediction for snap_scaffold_26-snap.1054-T1
Valid prediction for snap_scaffold_26-snap.1058-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55579-T1
Valid prediction for Augustus_model.g36811.t1
Couldn't classify 52745, 52924
Sorry, prediction pasa_asmbl_35594.p1 fails validation.
(ATG)	 GG	47532-48101	GT	AGG
(GTA)	 AG	49329-49624	GT	ATG
(GCC)	 AG	50191-50332	GT	AGG
(ATG)	 AG	51305-51388	GT	AGG
(ATA)	 AG	52745-52924	GG	CCG
-recovered pasa_asmbl_35594.p1, initial, 47532, 48101
-recovered pasa_asmbl_35594.p1, initial, 51305, 51388
-recovered pasa_asmbl_35594.p1, internal, 49329, 49624
-recovered pasa_asmbl_35594.p1, internal, 50191, 50332
-recovered pasa_asmbl_35594.p1, internal, 51305, 51388
Valid prediction for Augustus_model.g36818.t1
Valid prediction for Augustus_model.g36809.t1
Valid prediction for Augustus_model.g36819.t1
Valid prediction for snap_scaffold_26-snap.1060-T1
Valid prediction for snap_scaffold_26-snap.1061-T1
Valid prediction for Augustus_model.g36817.t1
Valid prediction for snap_scaffold_26-snap.1035-T1
Valid prediction for GlimmerHMM_glimmerT_55588-T1
Valid prediction for GlimmerHMM_glimmerT_55570-T1
Valid prediction for snap_scaffold_26-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_55581-T1
Valid prediction for Augustus_model.g36823.t1
Valid prediction for snap_scaffold_26-snap.1039-T1
Valid prediction for snap_scaffold_26-snap.1032-T1
Valid prediction for snap_scaffold_26-snap.1053-T1
Valid prediction for snap_scaffold_26-snap.1030-T1
Valid prediction for snap_scaffold_26-snap.1050-T1
Valid prediction for Augustus_model.g36822.t1
Valid prediction for CodingQuarry_transcript_40335-T1
Valid prediction for snap_scaffold_26-snap.1027-T1
Valid prediction for snap_scaffold_26-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_55584-T1
Valid prediction for GlimmerHMM_glimmerT_55585-T1
Valid prediction for snap_scaffold_26-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_55583-T1
Valid prediction for snap_scaffold_26-snap.1048-T1
Valid prediction for snap_scaffold_26-snap.1045-T1
Valid prediction for snap_scaffold_26-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_55572-T1
Valid prediction for Augustus_model.g36824.t1
Valid prediction for snap_scaffold_26-snap.1042-T1
Valid prediction for snap_scaffold_26-snap.1041-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 32921, rend_intergenic: 32918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20943, rend_intergenic: 17917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23223, rend_intergenic: 22042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25465, rend_intergenic: 23351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37592, rend_intergenic: 32918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67612, rend_intergenic: 64322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74650, rend_intergenic: 68714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130628, rend_intergenic: 127900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151987
-exon list size: 285


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.3    
6.6    
7.0    
7.3    
7.7    
8.0    
8.4    
8.7    
9.1    
9.4    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.3    
14.6    
15.0    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.8    
19.2    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.8    
27.2    
27.5    
27.9    
28.2    
28.6    
28.9    
29.3    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.7    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.2    
35.5    
35.9    
36.2    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.5    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.5    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.8    
64.1    
64.5    
64.8    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.3    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.7    
71.1    
71.4    
71.8    
72.1    
72.5    
72.8    
73.2    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.0    
85.4    
85.7    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.6    
90.9    
91.3    
91.6    
92.0    
92.3    
92.7    
93.0    
93.4    
93.7    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 32921, rend_intergenic: 32918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20943, rend_intergenic: 17917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23223, rend_intergenic: 22042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25465, rend_intergenic: 23351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37592, rend_intergenic: 32918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67612, rend_intergenic: 64322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74650, rend_intergenic: 68714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130628, rend_intergenic: 127900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support