-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_5007817-5184405

-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_3-snap.1093-T1
Valid prediction for Augustus_model.g4223.t1
Valid prediction for snap_scaffold_3-snap.1115-T1
Valid prediction for snap_scaffold_3-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_6517-T1
Valid prediction for snap_scaffold_3-snap.1094-T1
Valid prediction for Augustus_model.g4236.t1
Valid prediction for GlimmerHMM_glimmerT_6510-T1
Valid prediction for GlimmerHMM_glimmerT_6528-T1
Valid prediction for GlimmerHMM_glimmerT_6508-T1
Valid prediction for HiQ_model.g4224.t1
Valid prediction for GlimmerHMM_glimmerT_6504-T1
Valid prediction for Augustus_model.g4231.t1
Valid prediction for snap_scaffold_3-snap.1084-T1
Couldn't classify 31955, 32012
Sorry, prediction pasa_asmbl_40059.p1 fails validation.
(GGC)	 CA	31955-32012	GT	AGG
(GGA)	 AG	33712-33903	GT	GGG
(AGA)	 AG	34264-34440	GT	GGG
(ATA)	 AG	35717-35843	GT	GAG
(TGT)	 AG	36000-36121	GT	AGG
(TTC)	 AG	36586-36765	GT	ACG
(CTA)	 AG	37666-37799	GT	AGG
(CAT)	 AG	38455-38576	GT	AGG
(GTT)	 AG	38896-39076	CC	GAC
-recovered pasa_asmbl_40059.p1, terminal, 38896, 39076
-recovered pasa_asmbl_40059.p1, internal, 33712, 33903
-recovered pasa_asmbl_40059.p1, internal, 34264, 34440
-recovered pasa_asmbl_40059.p1, internal, 35717, 35843
-recovered pasa_asmbl_40059.p1, internal, 36000, 36121
-recovered pasa_asmbl_40059.p1, internal, 36586, 36765
-recovered pasa_asmbl_40059.p1, internal, 37666, 37799
-recovered pasa_asmbl_40059.p1, internal, 38455, 38576
Valid prediction for GlimmerHMM_glimmerT_6527-T1
Valid prediction for snap_scaffold_3-snap.1114-T1
Valid prediction for GlimmerHMM_glimmerT_6511-T1
Valid prediction for snap_scaffold_3-snap.1096-T1
Valid prediction for pasa_asmbl_40061.p2
Valid prediction for GlimmerHMM_glimmerT_6525-T1
Valid prediction for snap_scaffold_3-snap.1100-T1
Valid prediction for snap_scaffold_3-snap.1090-T1
Valid prediction for HiQ_model.g4226.t1
Valid prediction for snap_scaffold_3-snap.1097-T1
Valid prediction for Augustus_model.g4228.t1
Valid prediction for snap_scaffold_3-snap.1098-T1
Valid prediction for snap_scaffold_3-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_6514-T1
Valid prediction for snap_scaffold_3-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_6523-T1
Valid prediction for GlimmerHMM_glimmerT_6505-T1
Valid prediction for GlimmerHMM_glimmerT_6506-T1
Valid prediction for Augustus_model.g4230.t1
Valid prediction for snap_scaffold_3-snap.1092-T1
Valid prediction for CodingQuarry_transcript_46159-T1
Valid prediction for snap_scaffold_3-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_6518-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 Augustus_model.g4225.t1
Valid prediction for snap_scaffold_3-snap.1112-T1
Valid prediction for snap_scaffold_3-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_6521-T1
Valid prediction for GlimmerHMM_glimmerT_6526-T1
Valid prediction for GlimmerHMM_glimmerT_6524-T1
Valid prediction for Augustus_model.g4233.t1
Valid prediction for snap_scaffold_3-snap.1095-T1
Couldn't classify 35650, 35961
Sorry, prediction pasa_asmbl_38835.p3 fails validation.
(ATG)	 CG	35650-35961	AG	AAA
Valid prediction for snap_scaffold_3-snap.1088-T1
Valid prediction for snap_scaffold_3-snap.1109-T1
Valid prediction for snap_scaffold_3-snap.1102-T1
Valid prediction for snap_scaffold_3-snap.1082-T1
Valid prediction for snap_scaffold_3-snap.1106-T1
Valid prediction for Augustus_model.g4229.t1
Valid prediction for snap_scaffold_3-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_6512-T1
Valid prediction for Augustus_model.g4235.t1
Valid prediction for snap_scaffold_3-snap.1085-T1
Valid prediction for snap_scaffold_3-snap.1110-T1
Valid prediction for snap_scaffold_3-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_6513-T1
Valid prediction for GlimmerHMM_glimmerT_6507-T1
Valid prediction for snap_scaffold_3-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_6520-T1
Valid prediction for GlimmerHMM_glimmerT_6519-T1
Valid prediction for snap_scaffold_3-snap.1087-T1
Valid prediction for snap_scaffold_3-snap.1083-T1
Valid prediction for Augustus_model.g4222.t1
Valid prediction for GlimmerHMM_glimmerT_6502-T1
Couldn't classify 24356, 24517
Sorry, prediction pasa_asmbl_38836.p1 fails validation.
(GGT)	 AG	24356-24517	GT	TAG
(CCT)	 AG	24635-24850	GT	AGG
(GTG)	 AG	25083-25334	GT	TGG
(GCG)	 AG	27351-27501	GT	AGG
(TCC)	 AG	29583-29677	GT	AGG
(ATC)	 AG	30650-30664	CC	AAC
-recovered pasa_asmbl_38836.p1, terminal, 30650, 30664
-recovered pasa_asmbl_38836.p1, internal, 24356, 24517
-recovered pasa_asmbl_38836.p1, internal, 24635, 24850
-recovered pasa_asmbl_38836.p1, internal, 25083, 25334
-recovered pasa_asmbl_38836.p1, internal, 27351, 27501
-recovered pasa_asmbl_38836.p1, internal, 29583, 29677
Valid prediction for Augustus_model.g4227.t1
Valid prediction for Augustus_model.g4234.t1
Valid prediction for pasa_asmbl_38832.p1
Valid prediction for CodingQuarry_transcript_46160-T1
Valid prediction for snap_scaffold_3-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_6522-T1
Valid prediction for HiQ_model.g4232.t1
Valid prediction for GlimmerHMM_glimmerT_6515-T1
Valid prediction for snap_scaffold_3-snap.1101-T1
Valid prediction for snap_scaffold_3-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_6516-T1
Valid prediction for GlimmerHMM_glimmerT_6503-T1
Valid prediction for snap_scaffold_3-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_6509-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24961, rend_intergenic: 20296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37256, rend_intergenic: 28045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42795, rend_intergenic: 37778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52375, rend_intergenic: 42909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62145, rend_intergenic: 54655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72119, rend_intergenic: 70101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118680, rend_intergenic: 106567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160282, rend_intergenic: 154084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176589
-exon list size: 313


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.7    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.1    
12.4    
12.7    
13.0    
13.3    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.4    
19.7    
20.0    
20.3    
20.6    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.7    
27.0    
27.3    
27.6    
27.9    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.4    
39.7    
40.0    
40.3    
40.6    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.4    
59.7    
60.0    
60.3    
60.6    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.1    
72.4    
72.7    
73.0    
73.3    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.4    
79.7    
80.0    
80.3    
80.6    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.7    
87.0    
87.3    
87.6    
87.9    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.3    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 24961, rend_intergenic: 20296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37256, rend_intergenic: 28045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42795, rend_intergenic: 37778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52375, rend_intergenic: 42909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62145, rend_intergenic: 54655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72119, rend_intergenic: 70101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118680, rend_intergenic: 106567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160282, rend_intergenic: 154084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support