-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_10816179-11049476

-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_15-snap.2237-T1
Valid prediction for snap_scaffold_15-snap.2259-T1
Valid prediction for CodingQuarry_transcript_18135-T1
Valid prediction for GlimmerHMM_glimmerT_36910-T1
Valid prediction for HiQ_model.g24577.t1
Valid prediction for GlimmerHMM_glimmerT_36889-T1
Valid prediction for GlimmerHMM_glimmerT_36912-T1
Valid prediction for snap_scaffold_15-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_36914-T1
Valid prediction for snap_scaffold_15-snap.2246-T1
Valid prediction for GlimmerHMM_glimmerT_36886-T1
Valid prediction for HiQ_model.g24580.t1
Valid prediction for snap_scaffold_15-snap.2244-T1
Valid prediction for snap_scaffold_15-snap.2243-T1
Couldn't classify 22522, 22602
Sorry, prediction pasa_asmbl_15472.p1 fails validation.
(ATG)	 GC	21701-21843	GT	AGG
(GCA)	 AG	21990-22125	GT	AGG
(GAC)	 AG	22302-22382	GT	TGG
(GAG)	 AG	22522-22602	CT	AGC
-recovered pasa_asmbl_15472.p1, initial, 21701, 21843
-recovered pasa_asmbl_15472.p1, internal, 21990, 22125
-recovered pasa_asmbl_15472.p1, internal, 22302, 22382
Couldn't classify 18808, 18825
Couldn't classify 19820, 19855
Sorry, prediction pasa_asmbl_15923.p2 fails validation.
(GTG)	 CG	18808-18825	GT	ACG
(TCT)	 AG	18920-19039	GT	TGG
(GTA)	 AG	19277-19375	GT	AGG
(GCT)	 AG	19488-19634	GT	AGG
(ACC)	 AG	19820-19855	CT	ACC
-recovered pasa_asmbl_15923.p2, internal, 18920, 19039
-recovered pasa_asmbl_15923.p2, internal, 19277, 19375
-recovered pasa_asmbl_15923.p2, internal, 19488, 19634
Valid prediction for GlimmerHMM_glimmerT_36891-T1
Valid prediction for GlimmerHMM_glimmerT_36906-T1
Valid prediction for GlimmerHMM_glimmerT_36888-T1
Valid prediction for snap_scaffold_15-snap.2224-T1
Valid prediction for snap_scaffold_15-snap.2229-T1
Valid prediction for snap_scaffold_15-snap.2258-T1
Valid prediction for snap_scaffold_15-snap.2234-T1
Valid prediction for snap_scaffold_15-snap.2248-T1
Valid prediction for GlimmerHMM_glimmerT_36899-T1
Valid prediction for snap_scaffold_15-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_36896-T1
Valid prediction for GlimmerHMM_glimmerT_36913-T1
Valid prediction for snap_scaffold_15-snap.2260-T1
Valid prediction for CodingQuarry_transcript_18131-T1
Valid prediction for pasa_asmbl_15476.p1
Valid prediction for GlimmerHMM_glimmerT_36894-T1
Valid prediction for GlimmerHMM_glimmerT_36885-T1
Valid prediction for snap_scaffold_15-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_36900-T1
Valid prediction for snap_scaffold_15-snap.2255-T1
Valid prediction for GlimmerHMM_glimmerT_36909-T1
Valid prediction for snap_scaffold_15-snap.2239-T1
Valid prediction for GlimmerHMM_glimmerT_36904-T1
Valid prediction for Augustus_model.g24579.t1
Valid prediction for snap_scaffold_15-snap.2245-T1
Valid prediction for snap_scaffold_15-snap.2225-T1
Valid prediction for snap_scaffold_15-snap.2254-T1
Valid prediction for GlimmerHMM_glimmerT_36915-T1
Valid prediction for CodingQuarry_transcript_18137-T1
Valid prediction for GlimmerHMM_glimmerT_36911-T1
Valid prediction for GlimmerHMM_glimmerT_36898-T1
Valid prediction for Augustus_model.g24570.t1
Valid prediction for Augustus_model.g24585.t1
Valid prediction for HiQ_model.g24571.t1
Valid prediction for snap_scaffold_15-snap.2240-T1
Valid prediction for pasa_asmbl_15477.p1
Valid prediction for pasa_asmbl_15478.p1
Valid prediction for HiQ_model.g24572.t1
Valid prediction for snap_scaffold_15-snap.2241-T1
Valid prediction for Augustus_model.g24574.t1
Valid prediction for snap_scaffold_15-snap.2228-T1
Valid prediction for snap_scaffold_15-snap.2257-T1
Valid prediction for GlimmerHMM_glimmerT_36901-T1
Valid prediction for CodingQuarry_transcript_18130-T1
Valid prediction for GlimmerHMM_glimmerT_36895-T1
Valid prediction for Augustus_model.g24584.t1
Valid prediction for snap_scaffold_15-snap.2252-T1
Valid prediction for pasa_asmbl_15474.p1
Valid prediction for GlimmerHMM_glimmerT_36887-T1
Valid prediction for snap_scaffold_15-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_36902-T1
Valid prediction for snap_scaffold_15-snap.2231-T1
Couldn't classify 179054, 179368
Sorry, prediction pasa_asmbl_14469.p1 fails validation.
(TTC)	 CT	179054-179368	TT	GCT
Valid prediction for Augustus_model.g24582.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 GlimmerHMM_glimmerT_36903-T1
Valid prediction for snap_scaffold_15-snap.2247-T1
Valid prediction for snap_scaffold_15-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_36917-T1
Valid prediction for snap_scaffold_15-snap.2235-T1
Valid prediction for snap_scaffold_15-snap.2222-T1
Valid prediction for CodingQuarry_transcript_18134-T1
Valid prediction for snap_scaffold_15-snap.2253-T1
Valid prediction for snap_scaffold_15-snap.2238-T1
Valid prediction for CodingQuarry_transcript_18136-T1
Valid prediction for Augustus_model.g24573.t1
Valid prediction for snap_scaffold_15-snap.2220-T1
Couldn't classify 95950, 97144
Couldn't classify 99036, 99166
Sorry, prediction pasa_asmbl_14467.p1 fails validation.
(GCT)	 CA	95950-97144	GT	CGG
(GTG)	 AG	99036-99166	GG	ACG
Valid prediction for snap_scaffold_15-snap.2236-T1
Couldn't classify 141846, 141884
Sorry, prediction pasa_asmbl_14464.p1 fails validation.
(GAG)	 GG	141846-141884	GT	AGG
(GAG)	 AG	144650-144765	GT	GGG
(GTC)	 AG	145597-146029	AA	AAA
-recovered pasa_asmbl_14464.p1, terminal, 145597, 146029
-recovered pasa_asmbl_14464.p1, internal, 144650, 144765
Valid prediction for GlimmerHMM_glimmerT_36882-T1
Valid prediction for CodingQuarry_transcript_18132-T1
Valid prediction for Augustus_model.g24581.t1
Valid prediction for snap_scaffold_15-snap.2251-T1
Valid prediction for GlimmerHMM_glimmerT_36892-T1
Valid prediction for GlimmerHMM_glimmerT_36893-T1
Valid prediction for pasa_asmbl_14470.p1
Valid prediction for snap_scaffold_15-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_36907-T1
Valid prediction for GlimmerHMM_glimmerT_36908-T1
Valid prediction for snap_scaffold_15-snap.2250-T1
Valid prediction for Augustus_model.g24583.t1
Valid prediction for Augustus_model.g24586.t1
Valid prediction for Augustus_model.g24575.t1
Valid prediction for GlimmerHMM_glimmerT_36916-T1
Valid prediction for Augustus_model.g24569.t1
Valid prediction for snap_scaffold_15-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_36884-T1
Couldn't classify 167788, 167824
Sorry, prediction pasa_asmbl_14460.p1 fails validation.
(GCC)	 CA	167788-167824	GT	GGG
(GGA)	 AG	168542-168615	GT	AGG
(TGG)	 AG	169333-169446	GT	AGG
(GTG)	 AG	171383-171444	GT	AGG
(TGA)	 AG	173577-173682	GT	ACG
(GGG)	 AG	175485-175562	GA	AAG
-recovered pasa_asmbl_14460.p1, terminal, 175485, 175562
-recovered pasa_asmbl_14460.p1, internal, 168542, 168615
-recovered pasa_asmbl_14460.p1, internal, 169333, 169446
-recovered pasa_asmbl_14460.p1, internal, 171383, 171444
-recovered pasa_asmbl_14460.p1, internal, 173577, 173682
Valid prediction for snap_scaffold_15-snap.2256-T1
Couldn't classify 94235, 94906
Sorry, prediction pasa_asmbl_14468.p1 fails validation.
(GAC)	 CC	94235-94906	CC	GGC
Valid prediction for snap_scaffold_15-snap.2230-T1
Valid prediction for snap_scaffold_15-snap.2242-T1
Valid prediction for GlimmerHMM_glimmerT_36897-T1
Valid prediction for snap_scaffold_15-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_36883-T1
Valid prediction for HiQ_model.g24578.t1
Valid prediction for GlimmerHMM_glimmerT_36905-T1
Valid prediction for CodingQuarry_transcript_18133-T1
Couldn't classify 102531, 103178
Sorry, prediction pasa_asmbl_14466.p1 fails validation.
(AGG)	 AA	102531-103178	AC	AGA
Valid prediction for snap_scaffold_15-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_36890-T1
Couldn't classify 117261, 117371
Sorry, prediction pasa_asmbl_14465.p1 fails validation.
(GCT)	 TG	117261-117371	GT	AAG
(ATC)	 AG	117652-117746	GT	AGG
(GCA)	 AG	117835-117887	GT	CGG
(ATA)	 AG	118135-118241	TG	GAT
-recovered pasa_asmbl_14465.p1, terminal, 118135, 118241
-recovered pasa_asmbl_14465.p1, internal, 117652, 117746
-recovered pasa_asmbl_14465.p1, internal, 117835, 117887
Valid prediction for Augustus_model.g24568.t1
Valid prediction for GlimmerHMM_glimmerT_36881-T1
Valid prediction for Augustus_model.g24576.t1
Valid prediction for snap_scaffold_15-snap.2261-T1
Valid prediction for snap_scaffold_15-snap.2227-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 113102, rend_intergenic: 109171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120570, rend_intergenic: 119053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123907, rend_intergenic: 121545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153236, rend_intergenic: 136952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153981, rend_intergenic: 153293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159686, rend_intergenic: 154848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166396, rend_intergenic: 159919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175301, rend_intergenic: 168152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185596, rend_intergenic: 176569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199383, rend_intergenic: 185910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214511, rend_intergenic: 199859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221311, rend_intergenic: 214639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231489, rend_intergenic: 227028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233298
-exon list size: 452


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.4    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 113102, rend_intergenic: 109171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120570, rend_intergenic: 119053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123907, rend_intergenic: 121545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153236, rend_intergenic: 136952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153981, rend_intergenic: 153293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159686, rend_intergenic: 154848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166396, rend_intergenic: 159919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175301, rend_intergenic: 168152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185596, rend_intergenic: 176569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199383, rend_intergenic: 185910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214511, rend_intergenic: 199859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221311, rend_intergenic: 214639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231489, rend_intergenic: 227028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support