-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_15370631-15610093

-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.2950-T1
Valid prediction for GlimmerHMM_glimmerT_7882-T1
Couldn't classify 47222, 47394
Couldn't classify 49504, 49708
Sorry, prediction pasa_asmbl_40564.p1 fails validation.
(TTT)	 CG	47222-47394	GT	AGG
(CAA)	 AG	49504-49708	AA	GTA
Valid prediction for pasa_asmbl_40567.p1
Valid prediction for GlimmerHMM_glimmerT_7898-T1
Valid prediction for pasa_asmbl_40566.p1
Valid prediction for GlimmerHMM_glimmerT_7896-T1
Valid prediction for snap_scaffold_3-snap.2953-T1
Valid prediction for GlimmerHMM_glimmerT_7893-T1
Valid prediction for Augustus_model.g5209.t1
Valid prediction for GlimmerHMM_glimmerT_7875-T1
Valid prediction for snap_scaffold_3-snap.2941-T1
Valid prediction for snap_scaffold_3-snap.2968-T1
Valid prediction for HiQ_model.g5212.t1
Couldn't classify 73623, 73770
Sorry, prediction pasa_asmbl_40565.p1 fails validation.
(GGT)	 CA	73623-73770	GT	AGG
(GAT)	 AG	74457-74570	GT	AGG
(GGA)	 AG	76432-76520	CA	GAC
-recovered pasa_asmbl_40565.p1, terminal, 76432, 76520
-recovered pasa_asmbl_40565.p1, internal, 74457, 74570
Valid prediction for GlimmerHMM_glimmerT_7901-T1
Valid prediction for Augustus_model.g5211.t1
Valid prediction for snap_scaffold_3-snap.2946-T1
Valid prediction for snap_scaffold_3-snap.2969-T1
Valid prediction for snap_scaffold_3-snap.2967-T1
Valid prediction for GlimmerHMM_glimmerT_7885-T1
Valid prediction for GlimmerHMM_glimmerT_7891-T1
Valid prediction for snap_scaffold_3-snap.2962-T1
Valid prediction for CodingQuarry_transcript_46378-T1
Valid prediction for snap_scaffold_3-snap.2964-T1
Valid prediction for snap_scaffold_3-snap.2965-T1
Valid prediction for GlimmerHMM_glimmerT_7878-T1
Valid prediction for snap_scaffold_3-snap.2937-T1
Valid prediction for GlimmerHMM_glimmerT_7894-T1
Valid prediction for Augustus_model.g5213.t1
Valid prediction for Augustus_model.g5201.t1
Valid prediction for Augustus_model.g5202.t1
Valid prediction for snap_scaffold_3-snap.2951-T1
Valid prediction for HiQ_model.g5208.t1
Valid prediction for GlimmerHMM_glimmerT_7895-T1
Valid prediction for GlimmerHMM_glimmerT_7897-T1
Valid prediction for HiQ_model.g5200.t1
Valid prediction for Augustus_model.g5204.t1
Valid prediction for snap_scaffold_3-snap.2958-T1
Couldn't classify 201099, 201243
Couldn't classify 201360, 201374
Sorry, prediction CodingQuarry_transcript_46379-T1 fails validation.
(ATG)	 CC	199371-199463	GT	TGG
(GGT)	 AG	199804-199935	GT	GTG
(AAA)	 AG	200023-200070	GT	TGG
(ACA)	 AG	200158-200222	GT	AGG
(ACT)	 AG	200310-200374	GT	AGG
(ATG)	 AG	200517-200625	GT	ATG
(GGA)	 AG	201099-201243	CT	GCC
(AAG)	 AC	201360-201374	CC	AAC
-recovered CodingQuarry_transcript_46379-T1, initial, 199371, 199463
add_exon() Sorry, CodingQuarry_transcript_46379-T1 200517-200625-initial-1 is invalid.
-recovered CodingQuarry_transcript_46379-T1, initial, 200517, 200625
-recovered CodingQuarry_transcript_46379-T1, internal, 199804, 199935
-recovered CodingQuarry_transcript_46379-T1, internal, 200023, 200070
-recovered CodingQuarry_transcript_46379-T1, internal, 200158, 200222
-recovered CodingQuarry_transcript_46379-T1, internal, 200310, 200374
-recovered CodingQuarry_transcript_46379-T1, internal, 200517, 200625
Valid prediction for GlimmerHMM_glimmerT_7870-T1
Valid prediction for Augustus_model.g5207.t1
Valid prediction for snap_scaffold_3-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_7879-T1
Valid prediction for snap_scaffold_3-snap.2973-T1
Valid prediction for GlimmerHMM_glimmerT_7899-T1
Valid prediction for snap_scaffold_3-snap.2943-T1
Valid prediction for snap_scaffold_3-snap.2955-T1
Valid prediction for snap_scaffold_3-snap.2932-T1
Valid prediction for snap_scaffold_3-snap.2933-T1
Valid prediction for snap_scaffold_3-snap.2939-T1
Valid prediction for snap_scaffold_3-snap.2966-T1
Valid prediction for snap_scaffold_3-snap.2961-T1
Valid prediction for GlimmerHMM_glimmerT_7886-T1
Valid prediction for snap_scaffold_3-snap.2952-T1
Valid prediction for GlimmerHMM_glimmerT_7892-T1
Valid prediction for CodingQuarry_transcript_46380-T1
Valid prediction for snap_scaffold_3-snap.2934-T1
Valid prediction for snap_scaffold_3-snap.2963-T1
Valid prediction for snap_scaffold_3-snap.2960-T1
Valid prediction for Augustus_model.g5214.t1
Valid prediction for GlimmerHMM_glimmerT_7884-T1
Couldn't classify 57956, 58103
Couldn't classify 62144, 62289
Sorry, prediction pasa_asmbl_40870.p1 fails validation.
(GGT)	 CA	57956-58103	GT	AGG
(GTT)	 AG	58802-58924	GT	AGG
(GGC)	 AG	59726-59866	GT	TGG
(GAA)	 AG	61272-61412	GT	AGG
(GTC)	 AG	62144-62289	GG	GAG
-recovered pasa_asmbl_40870.p1, internal, 58802, 58924
-recovered pasa_asmbl_40870.p1, internal, 59726, 59866
-recovered pasa_asmbl_40870.p1, internal, 61272, 61412
Valid prediction for Augustus_model.g5210.t1
Valid prediction for GlimmerHMM_glimmerT_7890-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.g5196.t1
Valid prediction for GlimmerHMM_glimmerT_7888-T1
Valid prediction for GlimmerHMM_glimmerT_7902-T1
Valid prediction for snap_scaffold_3-snap.2947-T1
Valid prediction for snap_scaffold_3-snap.2942-T1
Valid prediction for GlimmerHMM_glimmerT_7900-T1
Valid prediction for snap_scaffold_3-snap.2972-T1
Valid prediction for GlimmerHMM_glimmerT_7877-T1
Valid prediction for snap_scaffold_3-snap.2970-T1
Valid prediction for GlimmerHMM_glimmerT_7889-T1
Valid prediction for GlimmerHMM_glimmerT_7874-T1
Valid prediction for Augustus_model.g5203.t1
Valid prediction for Augustus_model.g5205.t1
Valid prediction for snap_scaffold_3-snap.2945-T1
Valid prediction for GlimmerHMM_glimmerT_7880-T1
Valid prediction for Augustus_model.g5197.t1
Valid prediction for snap_scaffold_3-snap.2954-T1
Valid prediction for snap_scaffold_3-snap.2949-T1
Valid prediction for snap_scaffold_3-snap.2974-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g5198.t1
Valid prediction for GlimmerHMM_glimmerT_7872-T1
Valid prediction for snap_scaffold_3-snap.2957-T1
Valid prediction for Augustus_model.g5215.t1
Valid prediction for Augustus_model.g5206.t1
Valid prediction for GlimmerHMM_glimmerT_7881-T1
Valid prediction for GlimmerHMM_glimmerT_7871-T1
Valid prediction for GlimmerHMM_glimmerT_7873-T1
Valid prediction for Augustus_model.g5199.t1
Valid prediction for snap_scaffold_3-snap.2938-T1
Valid prediction for snap_scaffold_3-snap.2936-T1
Valid prediction for snap_scaffold_3-snap.2944-T1
Valid prediction for snap_scaffold_3-snap.2935-T1
Valid prediction for Augustus_model.g5195.t1
Valid prediction for snap_scaffold_3-snap.2948-T1
Valid prediction for GlimmerHMM_glimmerT_7887-T1
Valid prediction for snap_scaffold_3-snap.2940-T1
Valid prediction for snap_scaffold_3-snap.2956-T1
Valid prediction for GlimmerHMM_glimmerT_7883-T1
Valid prediction for snap_scaffold_3-snap.2959-T1
Valid prediction for GlimmerHMM_glimmerT_7876-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17787, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40044, rend_intergenic: 33762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62273, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 91070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153558, rend_intergenic: 152251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221810, rend_intergenic: 216882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225192, rend_intergenic: 222037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145337, rend_intergenic: 145334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239463
-exon list size: 340


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
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    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
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    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
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    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
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    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
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    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
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    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 17787, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40044, rend_intergenic: 33762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62273, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 91070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153558, rend_intergenic: 152251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221810, rend_intergenic: 216882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225192, rend_intergenic: 222037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 145337, rend_intergenic: 145334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support