-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_10333107-10552112

-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_2-snap.2047-T1
Valid prediction for snap_scaffold_2-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_4435-T1
Valid prediction for Augustus_model.g2968.t1
Valid prediction for snap_scaffold_2-snap.2025-T1
Valid prediction for snap_scaffold_2-snap.2039-T1
Valid prediction for snap_scaffold_2-snap.2057-T1
Valid prediction for snap_scaffold_2-snap.2037-T1
Valid prediction for snap_scaffold_2-snap.2035-T1
Valid prediction for Augustus_model.g2967.t1
Valid prediction for GlimmerHMM_glimmerT_4425-T1
Valid prediction for Augustus_model.g2971.t1
Valid prediction for GlimmerHMM_glimmerT_4418-T1
Valid prediction for snap_scaffold_2-snap.2059-T1
Valid prediction for GlimmerHMM_glimmerT_4438-T1
Valid prediction for snap_scaffold_2-snap.2043-T1
Valid prediction for Augustus_model.g2962.t1
Valid prediction for GlimmerHMM_glimmerT_4443-T1
Valid prediction for snap_scaffold_2-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_4424-T1
Valid prediction for snap_scaffold_2-snap.2022-T1
Valid prediction for Augustus_model.g2965.t1
Valid prediction for snap_scaffold_2-snap.2052-T1
Valid prediction for snap_scaffold_2-snap.2021-T1
Valid prediction for snap_scaffold_2-snap.2055-T1
Valid prediction for GlimmerHMM_glimmerT_4420-T1
Valid prediction for snap_scaffold_2-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_4430-T1
Valid prediction for GlimmerHMM_glimmerT_4439-T1
Valid prediction for snap_scaffold_2-snap.2045-T1
Valid prediction for CodingQuarry_transcript_28658-T1
Valid prediction for GlimmerHMM_glimmerT_4426-T1
Valid prediction for GlimmerHMM_glimmerT_4431-T1
Valid prediction for snap_scaffold_2-snap.2028-T1
Valid prediction for snap_scaffold_2-snap.2034-T1
Valid prediction for snap_scaffold_2-snap.2026-T1
Valid prediction for snap_scaffold_2-snap.2027-T1
Couldn't classify 59621, 60089
Couldn't classify 61866, 62051
Sorry, prediction pasa_asmbl_24703.p1 fails validation.
(GAA)	 CA	59621-60089	GT	CGG
(TCC)	 AG	60410-60534	GT	AAG
(CGT)	 AG	61866-62051	GA	AGG
-recovered pasa_asmbl_24703.p1, internal, 60410, 60534
Valid prediction for snap_scaffold_2-snap.2033-T1
Valid prediction for GlimmerHMM_glimmerT_4419-T1
Valid prediction for snap_scaffold_2-snap.2031-T1
Valid prediction for snap_scaffold_2-snap.2030-T1
Valid prediction for snap_scaffold_2-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_4432-T1
Valid prediction for snap_scaffold_2-snap.2060-T1
Valid prediction for Augustus_model.g2964.t1
Valid prediction for snap_scaffold_2-snap.2041-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.g2972.t1
Valid prediction for HiQ_model.g2960.t1
Valid prediction for Augustus_model.g2961.t1
Couldn't classify 183205, 183381
Sorry, prediction pasa_asmbl_23414.p1 fails validation.
(ATG)	 TT	181815-182882	GT	AGG
(GTG)	 AG	183205-183381	TA	ACT
-recovered pasa_asmbl_23414.p1, initial, 181815, 182882
Valid prediction for GlimmerHMM_glimmerT_4421-T1
Valid prediction for snap_scaffold_2-snap.2042-T1
Valid prediction for GlimmerHMM_glimmerT_4437-T1
Valid prediction for GlimmerHMM_glimmerT_4422-T1
Valid prediction for snap_scaffold_2-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_4440-T1
Valid prediction for Augustus_model.g2963.t1
Valid prediction for snap_scaffold_2-snap.2024-T1
Valid prediction for snap_scaffold_2-snap.2044-T1
Valid prediction for Augustus_model.g2958.t1
Valid prediction for GlimmerHMM_glimmerT_4423-T1
Valid prediction for snap_scaffold_2-snap.2049-T1
Valid prediction for GlimmerHMM_glimmerT_4429-T1
Valid prediction for GlimmerHMM_glimmerT_4442-T1
Valid prediction for Augustus_model.g2970.t1
Valid prediction for snap_scaffold_2-snap.2048-T1
Valid prediction for snap_scaffold_2-snap.2040-T1
Valid prediction for Augustus_model.g2966.t1
Valid prediction for GlimmerHMM_glimmerT_4433-T1
Valid prediction for snap_scaffold_2-snap.2032-T1
Valid prediction for Augustus_model.g2973.t1
Valid prediction for GlimmerHMM_glimmerT_4436-T1
Valid prediction for CodingQuarry_transcript_28657-T1
Valid prediction for snap_scaffold_2-snap.2054-T1
Couldn't classify 190548, 190661
Couldn't classify 192207, 192287
Sorry, prediction pasa_asmbl_23413.p1 fails validation.
(TAC)	 GC	190548-190661	GT	AGG
(ACC)	 AG	190857-190943	GT	ATG
(GTG)	 AG	191045-191229	GT	CAG
(CGT)	 AG	191779-191938	GT	AGG
(GCC)	 AG	192207-192287	AC	ACA
-recovered pasa_asmbl_23413.p1, internal, 190857, 190943
-recovered pasa_asmbl_23413.p1, internal, 191045, 191229
-recovered pasa_asmbl_23413.p1, internal, 191779, 191938
Valid prediction for snap_scaffold_2-snap.2051-T1
Valid prediction for snap_scaffold_2-snap.2029-T1
Valid prediction for snap_scaffold_2-snap.2056-T1
Valid prediction for Augustus_model.g2969.t1
Valid prediction for GlimmerHMM_glimmerT_4428-T1
Valid prediction for GlimmerHMM_glimmerT_4427-T1
Valid prediction for GlimmerHMM_glimmerT_4434-T1
Valid prediction for snap_scaffold_2-snap.2020-T1
Valid prediction for Augustus_model.g2959.t1
Valid prediction for pasa_asmbl_23415.p1
Couldn't classify 192661, 192711
Couldn't classify 196876, 196995
Sorry, prediction pasa_asmbl_23412.p1 fails validation.
(CAG)	 CC	192661-192711	GT	AGG
(CAG)	 AG	192929-193038	GT	GGG
(GAG)	 AG	193443-193610	GT	AGG
(GAG)	 AG	193834-194193	GT	AGG
(GTG)	 AG	194467-194619	GT	AGG
(TAT)	 AG	194747-194961	GT	AGG
(CCT)	 AG	196523-196644	GT	AGG
(GTG)	 AG	196876-196995	AC	CCA
-recovered pasa_asmbl_23412.p1, internal, 192929, 193038
-recovered pasa_asmbl_23412.p1, internal, 193443, 193610
-recovered pasa_asmbl_23412.p1, internal, 193834, 194193
-recovered pasa_asmbl_23412.p1, internal, 194467, 194619
-recovered pasa_asmbl_23412.p1, internal, 194747, 194961
-recovered pasa_asmbl_23412.p1, internal, 196523, 196644
Valid prediction for snap_scaffold_2-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_4441-T1
Valid prediction for CodingQuarry_transcript_28659-T1
Valid prediction for snap_scaffold_2-snap.2058-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 126009, rend_intergenic: 126006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37192, rend_intergenic: 26251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82666, rend_intergenic: 80555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91056, rend_intergenic: 83067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105078, rend_intergenic: 98620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131121, rend_intergenic: 126623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178387, rend_intergenic: 174165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189529, rend_intergenic: 179230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191995, rend_intergenic: 190265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200175, rend_intergenic: 192019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203830, rend_intergenic: 201845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208477, rend_intergenic: 204957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219006
-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 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 126009, rend_intergenic: 126006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37192, rend_intergenic: 26251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82666, rend_intergenic: 80555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91056, rend_intergenic: 83067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105078, rend_intergenic: 98620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131121, rend_intergenic: 126623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178387, rend_intergenic: 174165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189529, rend_intergenic: 179230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191995, rend_intergenic: 190265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200175, rend_intergenic: 192019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203830, rend_intergenic: 201845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208477, rend_intergenic: 204957  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

-building DP trellis

-building trellis in range 1 - 15877
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 206912 - 219006
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 207205 - 219006
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 207527 - 219006
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 208478 - 219006
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support