-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1676961-1861303

-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 Augustus_model.g38542.t1
Valid prediction for GlimmerHMM_glimmerT_58191-T1
Valid prediction for GlimmerHMM_glimmerT_58193-T1
Valid prediction for snap_scaffold_28-snap.438-T1
Valid prediction for snap_scaffold_28-snap.422-T1
Valid prediction for snap_scaffold_28-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_58197-T1
Valid prediction for snap_scaffold_28-snap.436-T1
Valid prediction for snap_scaffold_28-snap.431-T1
Valid prediction for snap_scaffold_28-snap.402-T1
Valid prediction for Augustus_model.g38531.t1
Valid prediction for GlimmerHMM_glimmerT_58212-T1
Valid prediction for snap_scaffold_28-snap.441-T1
Valid prediction for snap_scaffold_28-snap.410-T1
Valid prediction for Augustus_model.g38529.t1
Valid prediction for GlimmerHMM_glimmerT_58198-T1
Valid prediction for snap_scaffold_28-snap.401-T1
Valid prediction for snap_scaffold_28-snap.396-T1
Valid prediction for snap_scaffold_28-snap.399-T1
Valid prediction for GlimmerHMM_glimmerT_58200-T1
Valid prediction for snap_scaffold_28-snap.430-T1
Valid prediction for Augustus_model.g38545.t1
Valid prediction for GlimmerHMM_glimmerT_58222-T1
Valid prediction for snap_scaffold_28-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_58210-T1
Valid prediction for GlimmerHMM_glimmerT_58220-T1
Valid prediction for Augustus_model.g38537.t1
Valid prediction for GlimmerHMM_glimmerT_58206-T1
Valid prediction for GlimmerHMM_glimmerT_58214-T1
Valid prediction for Augustus_model.g38538.t1
Valid prediction for Augustus_model.g38533.t1
Valid prediction for Augustus_model.g38530.t1
Valid prediction for GlimmerHMM_glimmerT_58209-T1
Valid prediction for GlimmerHMM_glimmerT_58205-T1
Valid prediction for GlimmerHMM_glimmerT_58221-T1
Valid prediction for GlimmerHMM_glimmerT_58218-T1
Valid prediction for snap_scaffold_28-snap.428-T1
Valid prediction for snap_scaffold_28-snap.407-T1
Valid prediction for snap_scaffold_28-snap.391-T1
Valid prediction for snap_scaffold_28-snap.403-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58203-T1
Valid prediction for GlimmerHMM_glimmerT_58211-T1
Valid prediction for snap_scaffold_28-snap.397-T1
Valid prediction for Augustus_model.g38543.t1
Valid prediction for snap_scaffold_28-snap.418-T1
Valid prediction for Augustus_model.g38528.t1
Valid prediction for Augustus_model.g38540.t1
Valid prediction for Augustus_model.g38534.t1
Valid prediction for snap_scaffold_28-snap.420-T1
Valid prediction for snap_scaffold_28-snap.424-T1
Valid prediction for snap_scaffold_28-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_58208-T1
Valid prediction for snap_scaffold_28-snap.392-T1
Valid prediction for snap_scaffold_28-snap.433-T1
Valid prediction for snap_scaffold_28-snap.412-T1
Valid prediction for Augustus_model.g38524.t1
Valid prediction for GlimmerHMM_glimmerT_58216-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_58192-T1
Valid prediction for GlimmerHMM_glimmerT_58225-T1
Valid prediction for snap_scaffold_28-snap.429-T1
Valid prediction for CodingQuarry_transcript_43543-T1
Valid prediction for CodingQuarry_transcript_43542-T1
Valid prediction for Augustus_model.g38527.t1
Valid prediction for GlimmerHMM_glimmerT_58204-T1
Valid prediction for Augustus_model.g38539.t1
Valid prediction for GlimmerHMM_glimmerT_58228-T1
Valid prediction for snap_scaffold_28-snap.427-T1
Valid prediction for snap_scaffold_28-snap.413-T1
Valid prediction for snap_scaffold_28-snap.435-T1
Valid prediction for Augustus_model.g38523.t1
Valid prediction for snap_scaffold_28-snap.440-T1
Valid prediction for snap_scaffold_28-snap.395-T1
Couldn't classify 173734, 174031
Couldn't classify 175529, 175601
Sorry, prediction pasa_asmbl_38008.p1 fails validation.
(GGT)	 TA	173734-174031	GT	TGG
(ATG)	 AG	174635-174809	GT	AGG
(CCT)	 AG	175013-175167	GT	AGG
(AGA)	 AG	175281-175443	GT	AGG
(CGG)	 AG	175529-175601	GG	CTG
add_exon() Sorry, pasa_asmbl_38008.p1 174635-174809-initial-1 is invalid.
-recovered pasa_asmbl_38008.p1, initial, 174635, 174809
-recovered pasa_asmbl_38008.p1, internal, 174635, 174809
-recovered pasa_asmbl_38008.p1, internal, 175013, 175167
-recovered pasa_asmbl_38008.p1, internal, 175281, 175443
Valid prediction for snap_scaffold_28-snap.409-T1
Valid prediction for GlimmerHMM_glimmerT_58199-T1
Valid prediction for snap_scaffold_28-snap.439-T1
Valid prediction for snap_scaffold_28-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_58195-T1
Valid prediction for Augustus_model.g38525.t1
Valid prediction for snap_scaffold_28-snap.390-T1
Couldn't classify 156999, 157026
Sorry, prediction pasa_asmbl_38010.p1 fails validation.
(TTC)	 CC	156999-157026	GT	CGG
(GCT)	 AG	157993-158251	GT	AGG
(AGA)	 AG	158404-159712	CT	AGC
-recovered pasa_asmbl_38010.p1, terminal, 158404, 159712
-recovered pasa_asmbl_38010.p1, internal, 157993, 158251
Valid prediction for snap_scaffold_28-snap.437-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58189-T1
Valid prediction for GlimmerHMM_glimmerT_58190-T1
Valid prediction for snap_scaffold_28-snap.432-T1
Valid prediction for Augustus_model.g38532.t1
Valid prediction for Augustus_model.g38541.t1
Valid prediction for snap_scaffold_28-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_58227-T1
Couldn't classify 176512, 176556
Sorry, prediction pasa_asmbl_38006.p2 fails validation.
(GAC)	 TG	176512-176556	GT	AGG
(AAC)	 AG	176745-176832	GT	TGG
(ATT)	 AG	176960-177067	GT	AGG
(TTG)	 AG	177360-177432	GT	ATG
(GAA)	 AG	177687-177729	AA	GAA
-recovered pasa_asmbl_38006.p2, terminal, 177687, 177729
-recovered pasa_asmbl_38006.p2, internal, 176745, 176832
-recovered pasa_asmbl_38006.p2, internal, 176960, 177067
-recovered pasa_asmbl_38006.p2, internal, 177360, 177432
Valid prediction for CodingQuarry_transcript_43541-T1
Valid prediction for GlimmerHMM_glimmerT_58224-T1
Valid prediction for snap_scaffold_28-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_58202-T1
Valid prediction for snap_scaffold_28-snap.398-T1
Valid prediction for snap_scaffold_28-snap.416-T1
Valid prediction for snap_scaffold_28-snap.442-T1
Valid prediction for Augustus_model.g38526.t1
Valid prediction for GlimmerHMM_glimmerT_58207-T1
Couldn't classify 146391, 146587
Couldn't classify 147750, 147909
Sorry, prediction pasa_asmbl_38013.p1 fails validation.
(CCT)	 CA	146391-146587	GT	AGG
(ATA)	 AG	147750-147909	GG	CAG
Valid prediction for snap_scaffold_28-snap.404-T1
Couldn't classify 170944, 171009
Couldn't classify 173578, 173630
Sorry, prediction pasa_asmbl_38543.p1 fails validation.
(GTG)	 GG	170944-171009	GT	AGG
(GTT)	 AG	171529-171649	GT	AGG
(GGT)	 AG	172345-172444	GT	AGG
(CAC)	 AG	173303-173412	GT	GAG
(ATA)	 AG	173578-173630	AC	GAA
-recovered pasa_asmbl_38543.p1, internal, 171529, 171649
-recovered pasa_asmbl_38543.p1, internal, 172345, 172444
-recovered pasa_asmbl_38543.p1, internal, 173303, 173412
Valid prediction for snap_scaffold_28-snap.434-T1
Valid prediction for GlimmerHMM_glimmerT_58213-T1
Valid prediction for Augustus_model.g38535.t1
Valid prediction for snap_scaffold_28-snap.423-T1
Valid prediction for snap_scaffold_28-snap.414-T1
Valid prediction for snap_scaffold_28-snap.425-T1
Valid prediction for snap_scaffold_28-snap.426-T1
Valid prediction for GlimmerHMM_glimmerT_58188-T1
Valid prediction for Augustus_model.g38536.t1
Valid prediction for Augustus_model.g38544.t1
Valid prediction for snap_scaffold_28-snap.411-T1
Valid prediction for snap_scaffold_28-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_58217-T1
Valid prediction for GlimmerHMM_glimmerT_58219-T1
Valid prediction for snap_scaffold_28-snap.393-T1
Valid prediction for CodingQuarry_transcript_43540-T1
Valid prediction for snap_scaffold_28-snap.406-T1
Valid prediction for GlimmerHMM_glimmerT_58226-T1
Valid prediction for snap_scaffold_28-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_58196-T1
Valid prediction for GlimmerHMM_glimmerT_58223-T1
Valid prediction for GlimmerHMM_glimmerT_58194-T1
Valid prediction for GlimmerHMM_glimmerT_58215-T1
Valid prediction for Augustus_model.g38546.t1
Valid prediction for GlimmerHMM_glimmerT_58201-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52357, rend_intergenic: 47816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77731, rend_intergenic: 73088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83033, rend_intergenic: 80910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91042, rend_intergenic: 88764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96041, rend_intergenic: 91985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111725, rend_intergenic: 110043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119018, rend_intergenic: 114139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120701, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129537, rend_intergenic: 124399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147529, rend_intergenic: 146638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151912, rend_intergenic: 148975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170272, rend_intergenic: 167466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182497, rend_intergenic: 180888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184343
-exon list size: 388


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.1    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 52357, rend_intergenic: 47816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77731, rend_intergenic: 73088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83033, rend_intergenic: 80910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91042, rend_intergenic: 88764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96041, rend_intergenic: 91985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111725, rend_intergenic: 110043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119018, rend_intergenic: 114139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120701, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129537, rend_intergenic: 124399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147529, rend_intergenic: 146638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151912, rend_intergenic: 148975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170272, rend_intergenic: 167466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182497, rend_intergenic: 180888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support