-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_1673932-1915144

-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_7-snap.424-T1
Valid prediction for snap_scaffold_7-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_16933-T1
Valid prediction for GlimmerHMM_glimmerT_16944-T1
Valid prediction for snap_scaffold_7-snap.397-T1
Valid prediction for snap_scaffold_7-snap.428-T1
Valid prediction for snap_scaffold_7-snap.443-T1
Valid prediction for snap_scaffold_7-snap.399-T1
Valid prediction for Augustus_model.g11298.t1
Valid prediction for Augustus_model.g11314.t1
Valid prediction for snap_scaffold_7-snap.429-T1
Valid prediction for snap_scaffold_7-snap.439-T1
Valid prediction for snap_scaffold_7-snap.444-T1
Couldn't classify 9524, 9550
Sorry, prediction pasa_asmbl_49618.p2 fails validation.
(ATG)	 CG	5795-5981	GT	AGG
(GTC)	 AG	6855-6997	GT	AGG
(ACC)	 AG	9524-9550	GG	GAG
-recovered pasa_asmbl_49618.p2, initial, 5795, 5981
-recovered pasa_asmbl_49618.p2, internal, 6855, 6997
Valid prediction for snap_scaffold_7-snap.409-T1
Valid prediction for snap_scaffold_7-snap.403-T1
Valid prediction for snap_scaffold_7-snap.412-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16923-T1
Valid prediction for snap_scaffold_7-snap.427-T1
Valid prediction for GlimmerHMM_glimmerT_16930-T1
Valid prediction for GlimmerHMM_glimmerT_16921-T1
Valid prediction for Augustus_model.g11295.t1
Valid prediction for CodingQuarry_transcript_57445-T1
Valid prediction for snap_scaffold_7-snap.445-T1
Valid prediction for snap_scaffold_7-snap.411-T1
Valid prediction for pasa_asmbl_49623.p1
Valid prediction for Augustus_model.g11296.t1
Valid prediction for Augustus_model.g11303.t1
Valid prediction for snap_scaffold_7-snap.426-T1
Valid prediction for snap_scaffold_7-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_16946-T1
Valid prediction for snap_scaffold_7-snap.394-T1
Couldn't classify 20379, 21127
Couldn't classify 24875, 24982
Sorry, prediction pasa_asmbl_49622.p1 fails validation.
(CGC)	 GA	20379-21127	GT	ACG
(GTT)	 AG	21425-21707	GT	AGG
(GAC)	 AG	22350-22401	GT	AGG
(GGA)	 AG	22642-22750	GT	CGG
(GCT)	 AG	23948-24104	GT	ATG
(GTA)	 AG	24374-24490	GT	ACG
(ACT)	 AG	24599-24733	GT	AGG
(CCG)	 AG	24875-24982	CT	ACC
-recovered pasa_asmbl_49622.p1, internal, 21425, 21707
-recovered pasa_asmbl_49622.p1, internal, 22350, 22401
-recovered pasa_asmbl_49622.p1, internal, 22642, 22750
-recovered pasa_asmbl_49622.p1, internal, 23948, 24104
-recovered pasa_asmbl_49622.p1, internal, 24374, 24490
-recovered pasa_asmbl_49622.p1, internal, 24599, 24733
Valid prediction for snap_scaffold_7-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_16935-T1
Valid prediction for snap_scaffold_7-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_16929-T1
Valid prediction for snap_scaffold_7-snap.442-T1
Valid prediction for snap_scaffold_7-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_16947-T1
Valid prediction for snap_scaffold_7-snap.396-T1
Valid prediction for snap_scaffold_7-snap.416-T1
Couldn't classify 19630, 19688
Sorry, prediction pasa_asmbl_49620.p1 fails validation.
(ATG)	 TC	18446-18683	GT	AGG
(GTG)	 AG	19009-19128	GT	AAG
(ATC)	 AG	19630-19688	GC	TGG
-recovered pasa_asmbl_49620.p1, initial, 18446, 18683
-recovered pasa_asmbl_49620.p1, internal, 19009, 19128
-recovered pasa_asmbl_49620.p1, internal, 19630, 19688
Valid prediction for Augustus_model.g11294.t1
Valid prediction for GlimmerHMM_glimmerT_16925-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_7-snap.425-T1
Valid prediction for snap_scaffold_7-snap.401-T1
Valid prediction for snap_scaffold_7-snap.441-T1
Valid prediction for Augustus_model.g11309.t1
Valid prediction for snap_scaffold_7-snap.432-T1
Valid prediction for Augustus_model.g11300.t1
Valid prediction for snap_scaffold_7-snap.431-T1
Valid prediction for snap_scaffold_7-snap.419-T1
Valid prediction for snap_scaffold_7-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_16931-T1
Valid prediction for Augustus_model.g11313.t1
Valid prediction for GlimmerHMM_glimmerT_16926-T1
Valid prediction for snap_scaffold_7-snap.414-T1
Valid prediction for Augustus_model.g11310.t1
Valid prediction for GlimmerHMM_glimmerT_16945-T1
Valid prediction for Augustus_model.g11305.t1
Valid prediction for Augustus_model.g11299.t1
Valid prediction for Augustus_model.g11307.t1
Valid prediction for GlimmerHMM_glimmerT_16924-T1
Valid prediction for GlimmerHMM_glimmerT_16920-T1
Valid prediction for GlimmerHMM_glimmerT_16927-T1
Valid prediction for snap_scaffold_7-snap.423-T1
Valid prediction for snap_scaffold_7-snap.435-T1
Valid prediction for Augustus_model.g11301.t1
Valid prediction for snap_scaffold_7-snap.430-T1
Valid prediction for snap_scaffold_7-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_16939-T1
Valid prediction for snap_scaffold_7-snap.405-T1
Valid prediction for Augustus_model.g11311.t1
Valid prediction for snap_scaffold_7-snap.404-T1
Valid prediction for snap_scaffold_7-snap.434-T1
Valid prediction for GlimmerHMM_glimmerT_16934-T1
Valid prediction for Augustus_model.g11302.t1
Valid prediction for GlimmerHMM_glimmerT_16928-T1
Valid prediction for snap_scaffold_7-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_16937-T1
Valid prediction for snap_scaffold_7-snap.413-T1
Valid prediction for snap_scaffold_7-snap.408-T1
Valid prediction for snap_scaffold_7-snap.437-T1
Valid prediction for GlimmerHMM_glimmerT_16938-T1
Valid prediction for GlimmerHMM_glimmerT_16942-T1
Valid prediction for snap_scaffold_7-snap.420-T1
Valid prediction for snap_scaffold_7-snap.406-T1
Valid prediction for Augustus_model.g11304.t1
Valid prediction for GlimmerHMM_glimmerT_16943-T1
Valid prediction for snap_scaffold_7-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_16922-T1
Valid prediction for GlimmerHMM_glimmerT_16936-T1
Valid prediction for snap_scaffold_7-snap.436-T1
Valid prediction for GlimmerHMM_glimmerT_16932-T1
Valid prediction for snap_scaffold_7-snap.433-T1
Valid prediction for snap_scaffold_7-snap.418-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g11312.t1
Valid prediction for snap_scaffold_7-snap.417-T1
Valid prediction for snap_scaffold_7-snap.422-T1
Valid prediction for snap_scaffold_7-snap.400-T1
Valid prediction for Augustus_model.g11306.t1
Valid prediction for Augustus_model.g11297.t1
Valid prediction for GlimmerHMM_glimmerT_16940-T1
Valid prediction for GlimmerHMM_glimmerT_16941-T1
Valid prediction for Augustus_model.g11308.t1
Valid prediction for snap_scaffold_7-snap.410-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42264, rend_intergenic: 36548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81931, rend_intergenic: 79587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103611, rend_intergenic: 101090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136178, rend_intergenic: 127960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185563, rend_intergenic: 180531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241213
-exon list size: 368


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 42264, rend_intergenic: 36548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81931, rend_intergenic: 79587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103611, rend_intergenic: 101090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136178, rend_intergenic: 127960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185563, rend_intergenic: 180531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 222456 - 241213
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 222456 - 236759
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 224157 - 236759
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 224157 - 235483
-exon list size: 1


building trellis

33.3    
66.7    
-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