-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_3840258-4048338

-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_29152-T1
Valid prediction for snap_scaffold_12-snap.803-T1
Valid prediction for snap_scaffold_12-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_29167-T1
Valid prediction for Augustus_model.g19231.t1
Valid prediction for snap_scaffold_12-snap.822-T1
Couldn't classify 122834, 122917
Sorry, prediction pasa_asmbl_7578.p1 fails validation.
(GCG)	 TG	122834-122917	GC	AGG
(GAG)	 AG	123747-123852	GT	TTG
(TCT)	 AG	124195-124347	GT	GAG
(GTG)	 AG	124475-124546	GT	AGG
(ACT)	 AG	124746-124851	GT	AGG
(TTC)	 AG	125044-125086	GT	AGG
(CAG)	 AG	125637-125723	GT	AGG
(GTC)	 AG	126286-126366	GT	AGG
(GCT)	 AG	126726-126776	AA	AAA
-recovered pasa_asmbl_7578.p1, terminal, 126726, 126776
-recovered pasa_asmbl_7578.p1, internal, 123747, 123852
-recovered pasa_asmbl_7578.p1, internal, 124195, 124347
-recovered pasa_asmbl_7578.p1, internal, 124475, 124546
-recovered pasa_asmbl_7578.p1, internal, 124746, 124851
-recovered pasa_asmbl_7578.p1, internal, 125044, 125086
-recovered pasa_asmbl_7578.p1, internal, 125637, 125723
-recovered pasa_asmbl_7578.p1, internal, 126286, 126366
Valid prediction for GlimmerHMM_glimmerT_29146-T1
Valid prediction for snap_scaffold_12-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_29156-T1
Valid prediction for GlimmerHMM_glimmerT_29159-T1
Valid prediction for CodingQuarry_transcript_10167-T1
Valid prediction for snap_scaffold_12-snap.790-T1
Valid prediction for GlimmerHMM_glimmerT_29165-T1
Valid prediction for snap_scaffold_12-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_29166-T1
Valid prediction for Augustus_model.g19229.t1
Valid prediction for snap_scaffold_12-snap.792-T1
Valid prediction for GlimmerHMM_glimmerT_29163-T1
Valid prediction for Augustus_model.g19241.t1
Valid prediction for snap_scaffold_12-snap.796-T1
Valid prediction for snap_scaffold_12-snap.816-T1
Valid prediction for snap_scaffold_12-snap.798-T1
Valid prediction for CodingQuarry_transcript_10166-T1
Valid prediction for snap_scaffold_12-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_29148-T1
Valid prediction for Augustus_model.g19239.t1
Couldn't classify 58933, 59025
Sorry, prediction pasa_asmbl_7576.p1 fails validation.
(ATG)	 AG	54920-54971	GT	TGG
(GTT)	 AG	55265-55347	GT	CAG
(GTG)	 AG	55719-55838	GT	GTG
(TTG)	 AG	56268-56361	GT	CAG
(GTG)	 AG	56542-56639	GT	CGG
(AAA)	 AG	56909-56982	GT	GAG
(TGA)	 AG	57085-57160	GT	AGG
(AGC)	 AG	58933-59025	GT	AGG
-recovered pasa_asmbl_7576.p1, initial, 54920, 54971
add_exon() Sorry, pasa_asmbl_7576.p1 56909-56982-terminal-2 is invalid.
-recovered pasa_asmbl_7576.p1, terminal, 56909, 56982
-recovered pasa_asmbl_7576.p1, internal, 54920, 54971
-recovered pasa_asmbl_7576.p1, internal, 55265, 55347
-recovered pasa_asmbl_7576.p1, internal, 55719, 55838
-recovered pasa_asmbl_7576.p1, internal, 56268, 56361
-recovered pasa_asmbl_7576.p1, internal, 56542, 56639
-recovered pasa_asmbl_7576.p1, internal, 56909, 56982
-recovered pasa_asmbl_7576.p1, internal, 57085, 57160
-recovered pasa_asmbl_7576.p1, internal, 58933, 59025
Valid prediction for snap_scaffold_12-snap.821-T1
Valid prediction for snap_scaffold_12-snap.806-T1
Valid prediction for GlimmerHMM_glimmerT_29150-T1
Valid prediction for snap_scaffold_12-snap.815-T1
Valid prediction for snap_scaffold_12-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_29161-T1
Valid prediction for Augustus_model.g19236.t1
Valid prediction for Augustus_model.g19243.t1
Valid prediction for snap_scaffold_12-snap.809-T1
Valid prediction for GlimmerHMM_glimmerT_29153-T1
Valid prediction for snap_scaffold_12-snap.785-T1
Valid prediction for GlimmerHMM_glimmerT_29164-T1
Valid prediction for Augustus_model.g19238.t1
Valid prediction for Augustus_model.g19234.t1
Valid prediction for GlimmerHMM_glimmerT_29149-T1
Valid prediction for snap_scaffold_12-snap.786-T1
Valid prediction for snap_scaffold_12-snap.814-T1
Valid prediction for CodingQuarry_transcript_10168-T1
Valid prediction for GlimmerHMM_glimmerT_29160-T1
Valid prediction for snap_scaffold_12-snap.810-T1
Valid prediction for snap_scaffold_12-snap.791-T1
Valid prediction for GlimmerHMM_glimmerT_29145-T1
Valid prediction for snap_scaffold_12-snap.812-T1
Valid prediction for HiQ_model.g19233.t1
Valid prediction for snap_scaffold_12-snap.794-T1
Valid prediction for snap_scaffold_12-snap.800-T1
Couldn't classify 47724, 47945
Sorry, prediction Augustus_model.g19232.t1 fails validation.
(CGG)	 AG	47724-47945	GT	AGG
(CAG)	 AG	48323-48560	GT	AGG
(GAG)	 AG	50058-50274	CT	GAC
-recovered Augustus_model.g19232.t1, terminal, 50058, 50274
-recovered Augustus_model.g19232.t1, internal, 47724, 47945
-recovered Augustus_model.g19232.t1, internal, 48323, 48560

-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: -)Couldn't classify 77221, 77386
Sorry, prediction pasa_asmbl_8378.p1 fails validation.
(AAA)	 AG	77221-77386	GT	AGG
(GTC)	 AG	78018-78478	CT	GAC
-recovered pasa_asmbl_8378.p1, terminal, 78018, 78478
-recovered pasa_asmbl_8378.p1, internal, 77221, 77386
Valid prediction for GlimmerHMM_glimmerT_29168-T1
Valid prediction for snap_scaffold_12-snap.804-T1
Valid prediction for GlimmerHMM_glimmerT_29158-T1
Valid prediction for GlimmerHMM_glimmerT_29155-T1
Valid prediction for snap_scaffold_12-snap.807-T1
Valid prediction for snap_scaffold_12-snap.787-T1
Valid prediction for Augustus_model.g19228.t1
Valid prediction for snap_scaffold_12-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_29142-T1
Valid prediction for snap_scaffold_12-snap.819-T1
Valid prediction for snap_scaffold_12-snap.808-T1
Valid prediction for snap_scaffold_12-snap.820-T1
Valid prediction for GlimmerHMM_glimmerT_29144-T1
Valid prediction for snap_scaffold_12-snap.817-T1
Valid prediction for Augustus_model.g19230.t1
Valid prediction for snap_scaffold_12-snap.811-T1
Valid prediction for snap_scaffold_12-snap.795-T1
Valid prediction for HiQ_model.g19240.t1
Valid prediction for GlimmerHMM_glimmerT_29143-T1
Valid prediction for snap_scaffold_12-snap.801-T1
Valid prediction for GlimmerHMM_glimmerT_29154-T1
Valid prediction for snap_scaffold_12-snap.805-T1
Valid prediction for Augustus_model.g19244.t1
Valid prediction for snap_scaffold_12-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_29151-T1
Valid prediction for snap_scaffold_12-snap.813-T1
Valid prediction for snap_scaffold_12-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_29157-T1
Valid prediction for Augustus_model.g19235.t1
Valid prediction for Augustus_model.g19242.t1
Valid prediction for snap_scaffold_12-snap.823-T1
Valid prediction for GlimmerHMM_glimmerT_29147-T1
Valid prediction for Augustus_model.g19237.t1
Valid prediction for GlimmerHMM_glimmerT_29162-T1
Valid prediction for snap_scaffold_12-snap.784-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18364, rend_intergenic: 15501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59079, rend_intergenic: 55647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72105, rend_intergenic: 68598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75216, rend_intergenic: 73470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79197, rend_intergenic: 76158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104013, rend_intergenic: 101434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115912, rend_intergenic: 111964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143981, rend_intergenic: 140448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156554, rend_intergenic: 152518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160861, rend_intergenic: 159459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204473, rend_intergenic: 200756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208081
-exon list size: 269


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.5    
5.9    
6.3    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.9    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.0    
14.4    
14.8    
15.1    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.5    
18.8    
19.2    
19.6    
19.9    
20.3    
20.7    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.2    
23.6    
24.0    
24.4    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
26.9    
27.3    
27.7    
28.0    
28.4    
28.8    
29.2    
29.5    
29.9    
30.3    
30.6    
31.0    
31.4    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.5    
39.9    
40.2    
40.6    
41.0    
41.3    
41.7    
42.1    
42.4    
42.8    
43.2    
43.5    
43.9    
44.3    
44.6    
45.0    
45.4    
45.8    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.2    
54.6    
55.0    
55.4    
55.7    
56.1    
56.5    
56.8    
57.2    
57.6    
57.9    
58.3    
58.7    
59.0    
59.4    
59.8    
60.1    
60.5    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.6    
69.0    
69.4    
69.7    
70.1    
70.5    
70.8    
71.2    
71.6    
72.0    
72.3    
72.7    
73.1    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.8    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.3    
79.7    
80.1    
80.4    
80.8    
81.2    
81.5    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.9    
85.2    
85.6    
86.0    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.1    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.7    
94.1    
94.5    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 18364, rend_intergenic: 15501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59079, rend_intergenic: 55647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72105, rend_intergenic: 68598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75216, rend_intergenic: 73470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79197, rend_intergenic: 76158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104013, rend_intergenic: 101434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115912, rend_intergenic: 111964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143981, rend_intergenic: 140448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156554, rend_intergenic: 152518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160861, rend_intergenic: 159459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204473, rend_intergenic: 200756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support