-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_17234437-17395788

-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.41578_t
Valid prediction for GeneMark_model.41574_t
Valid prediction for snap_scaffold_9-snap.3514-T1
Valid prediction for snap_scaffold_9-snap.3492-T1
Valid prediction for GeneMark_model.41553_t
Valid prediction for Augustus_model.g16218.t1
Valid prediction for GlimmerHMM_glimmerT_24232-T1
Valid prediction for GlimmerHMM_glimmerT_24231-T1
Valid prediction for snap_scaffold_9-snap.3497-T1
Couldn't classify 122393, 122607
Couldn't classify 123709, 123905
Sorry, prediction pasa_asmbl_54604.p1 fails validation.
(GAG)	 AG	122393-122607	GT	AGG
(TCG)	 AG	123163-123317	GT	AGG
(ACC)	 AG	123709-123905	AG	TCA
add_exon() Sorry, pasa_asmbl_54604.p1 122393-122607-terminal-2 is invalid.
-recovered pasa_asmbl_54604.p1, terminal, 122393, 122607
-recovered pasa_asmbl_54604.p1, internal, 122393, 122607
-recovered pasa_asmbl_54604.p1, internal, 123163, 123317
Valid prediction for GeneMark_model.41568_t
Valid prediction for GlimmerHMM_glimmerT_24235-T1
Valid prediction for GeneMark_model.41556_t
Valid prediction for GeneMark_model.41564_t
Valid prediction for snap_scaffold_9-snap.3502-T1
Valid prediction for GeneMark_model.41554_t
Valid prediction for snap_scaffold_9-snap.3499-T1
Valid prediction for snap_scaffold_9-snap.3507-T1
Valid prediction for GeneMark_model.41579_t
Valid prediction for GeneMark_model.41561_t
Valid prediction for GeneMark_model.41570_t
Valid prediction for snap_scaffold_9-snap.3519-T1
Valid prediction for snap_scaffold_9-snap.3494-T1
Valid prediction for snap_scaffold_9-snap.3506-T1
Valid prediction for GlimmerHMM_glimmerT_24236-T1
Valid prediction for GeneMark_model.41562_t
Valid prediction for snap_scaffold_9-snap.3511-T1
Valid prediction for GeneMark_model.41555_t
Valid prediction for GeneMark_model.41558_t
Valid prediction for GeneMark_model.41576_t
Valid prediction for GeneMark_model.41550_t
Valid prediction for GeneMark_model.41551_t
Valid prediction for GeneMark_model.41572_t
Valid prediction for GeneMark_model.41582_t
Valid prediction for GeneMark_model.41565_t
Valid prediction for GlimmerHMM_glimmerT_24233-T1
Valid prediction for Augustus_model.g16224.t1
Valid prediction for snap_scaffold_9-snap.3500-T1
Valid prediction for GlimmerHMM_glimmerT_24229-T1
Valid prediction for snap_scaffold_9-snap.3512-T1
Valid prediction for HiQ_model.g16222.t1
Valid prediction for GlimmerHMM_glimmerT_24240-T1
Valid prediction for Augustus_model.g16227.t1
Valid prediction for Augustus_model.g16221.t1
Valid prediction for pasa_asmbl_54605.p1
Valid prediction for GeneMark_model.41580_t
Valid prediction for snap_scaffold_9-snap.3518-T1
Valid prediction for snap_scaffold_9-snap.3503-T1
Valid prediction for GlimmerHMM_glimmerT_24243-T1
Valid prediction for snap_scaffold_9-snap.3516-T1
Valid prediction for GlimmerHMM_glimmerT_24238-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.3513-T1
Valid prediction for snap_scaffold_9-snap.3495-T1
Valid prediction for Augustus_model.g16226.t1
Valid prediction for snap_scaffold_9-snap.3508-T1
Valid prediction for GeneMark_model.41581_t
Valid prediction for snap_scaffold_9-snap.3515-T1
Valid prediction for snap_scaffold_9-snap.3509-T1
Valid prediction for GlimmerHMM_glimmerT_24241-T1
Valid prediction for GeneMark_model.41566_t
Valid prediction for Augustus_model.g16219.t1
Valid prediction for GeneMark_model.41567_t
Valid prediction for GlimmerHMM_glimmerT_24237-T1
Valid prediction for snap_scaffold_9-snap.3498-T1
Couldn't classify 91165, 91284
Sorry, prediction pasa_asmbl_55599.p1 fails validation.
(GGC)	 CA	91165-91284	GT	AGG
(GTG)	 AG	91573-91788	AA	GAA
-recovered pasa_asmbl_55599.p1, terminal, 91573, 91788
Valid prediction for GeneMark_model.41563_t
Valid prediction for snap_scaffold_9-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_24230-T1
Valid prediction for snap_scaffold_9-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_24234-T1
Valid prediction for GeneMark_model.41552_t
Valid prediction for GlimmerHMM_glimmerT_24242-T1
Valid prediction for GlimmerHMM_glimmerT_24239-T1
Valid prediction for Augustus_model.g16220.t1
Valid prediction for Augustus_model.g16223.t1
Valid prediction for GeneMark_model.41571_t
Valid prediction for snap_scaffold_9-snap.3491-T1
Valid prediction for GeneMark_model.41560_t
Valid prediction for GeneMark_model.41559_t
Valid prediction for GeneMark_model.41573_t
Couldn't classify 84378, 84498
Couldn't classify 87639, 87898
Sorry, prediction pasa_asmbl_55600.p1 fails validation.
(GAT)	 CA	84378-84498	GT	AGG
(ATC)	 AG	85072-85272	GT	AGG
(AAG)	 AG	85596-85676	GT	CAG
(GCT)	 AG	85955-86200	GT	AGG
(GTA)	 AG	87639-87898	GG	CAG
-recovered pasa_asmbl_55600.p1, internal, 85072, 85272
-recovered pasa_asmbl_55600.p1, internal, 85596, 85676
-recovered pasa_asmbl_55600.p1, internal, 85955, 86200
Valid prediction for snap_scaffold_9-snap.3504-T1
Valid prediction for snap_scaffold_9-snap.3493-T1
Valid prediction for GlimmerHMM_glimmerT_24228-T1
Valid prediction for snap_scaffold_9-snap.3496-T1
Valid prediction for GeneMark_model.41575_t
Valid prediction for GeneMark_model.41557_t
Valid prediction for Augustus_model.g16225.t1
Valid prediction for snap_scaffold_9-snap.3517-T1
Valid prediction for snap_scaffold_9-snap.3501-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 94238, rend_intergenic: 94235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31614, rend_intergenic: 29783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38959, rend_intergenic: 32750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79920, rend_intergenic: 79202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128458, rend_intergenic: 126682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161352
-exon list size: 329


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 94238, rend_intergenic: 94235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31614, rend_intergenic: 29783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38959, rend_intergenic: 32750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79920, rend_intergenic: 79202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128458, rend_intergenic: 126682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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