-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_13024656-13206813

-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_8-snap.2372-T1
Valid prediction for snap_scaffold_8-snap.2382-T1
Valid prediction for HiQ_model.g13804.t1
Valid prediction for GlimmerHMM_glimmerT_20674-T1
Valid prediction for snap_scaffold_8-snap.2365-T1
Valid prediction for Augustus_model.g13796.t1
Valid prediction for snap_scaffold_8-snap.2368-T1
Valid prediction for Augustus_model.g13798.t1
Valid prediction for pasa_asmbl_53610.p1
Couldn't classify 103782, 104177
Sorry, prediction pasa_asmbl_53349.p1 fails validation.
(GGT)	 GT	103782-104177	TG	GAT
Valid prediction for snap_scaffold_8-snap.2379-T1
Valid prediction for snap_scaffold_8-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_20680-T1
Valid prediction for snap_scaffold_8-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_20670-T1
Valid prediction for snap_scaffold_8-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_20689-T1
Valid prediction for GlimmerHMM_glimmerT_20676-T1
Valid prediction for GlimmerHMM_glimmerT_20673-T1
Valid prediction for Augustus_model.g13805.t1
Valid prediction for snap_scaffold_8-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_20690-T1
Couldn't classify 96691, 96905
Couldn't classify 99010, 99031
Sorry, prediction pasa_asmbl_53614.p1 fails validation.
(CGT)	 GA	96691-96905	GT	CTG
(GCA)	 AG	97631-97702	GT	CTG
(GGA)	 AG	99010-99031	AA	TCA
-recovered pasa_asmbl_53614.p1, internal, 97631, 97702
Valid prediction for Augustus_model.g13800.t1
Valid prediction for Augustus_model.g13799.t1
Valid prediction for snap_scaffold_8-snap.2354-T1
Valid prediction for GlimmerHMM_glimmerT_20672-T1
Valid prediction for snap_scaffold_8-snap.2385-T1
Valid prediction for snap_scaffold_8-snap.2383-T1
Valid prediction for CodingQuarry_transcript_59882-T1
Valid prediction for snap_scaffold_8-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_20681-T1
Valid prediction for snap_scaffold_8-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_20675-T1
Valid prediction for snap_scaffold_8-snap.2374-T1
Valid prediction for snap_scaffold_8-snap.2353-T1
Valid prediction for GlimmerHMM_glimmerT_20671-T1
Valid prediction for Augustus_model.g13797.t1
Valid prediction for snap_scaffold_8-snap.2364-T1
Valid prediction for snap_scaffold_8-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_20686-T1
Valid prediction for snap_scaffold_8-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_20666-T1
Valid prediction for GlimmerHMM_glimmerT_20679-T1
Valid prediction for GlimmerHMM_glimmerT_20684-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_20667-T1
Valid prediction for GlimmerHMM_glimmerT_20677-T1
Valid prediction for snap_scaffold_8-snap.2380-T1
Valid prediction for snap_scaffold_8-snap.2358-T1
Valid prediction for snap_scaffold_8-snap.2366-T1
Valid prediction for pasa_asmbl_52280.p1
Valid prediction for snap_scaffold_8-snap.2363-T1
Valid prediction for Augustus_model.g13806.t1
Valid prediction for snap_scaffold_8-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_20669-T1
Valid prediction for CodingQuarry_transcript_59876-T1
Valid prediction for CodingQuarry_transcript_59877-T1
Valid prediction for CodingQuarry_transcript_59878-T1
Valid prediction for HiQ_model.g13803.t1
Valid prediction for Augustus_model.g13807.t1
Valid prediction for GlimmerHMM_glimmerT_20685-T1
Valid prediction for CodingQuarry_transcript_59881-T1
Valid prediction for snap_scaffold_8-snap.2362-T1
Valid prediction for snap_scaffold_8-snap.2352-T1
Valid prediction for GlimmerHMM_glimmerT_20668-T1
Valid prediction for snap_scaffold_8-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_20682-T1
Valid prediction for snap_scaffold_8-snap.2355-T1
Valid prediction for snap_scaffold_8-snap.2384-T1
Valid prediction for HiQ_model.g13801.t1
Valid prediction for snap_scaffold_8-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_20678-T1
Valid prediction for snap_scaffold_8-snap.2359-T1
Couldn't classify 49803, 50072
Sorry, prediction Augustus_model.g13802.t1 fails validation.
(TCT)	 AG	49803-50072	GT	AGG
(AAG)	 AG	51077-51301	GT	GGG
(AGG)	 AG	51484-51561	GT	GGG
(GTG)	 AG	51784-51932	GT	AGG
(ATA)	 AG	52060-52177	GT	TGG
(AGG)	 AG	52313-52361	GT	ACG
(TAG)	 AG	53712-53771	GT	AGG
(GGC)	 AG	55696-55859	GT	AGG
(CTT)	 AG	56102-56234	GT	AGG
(ATA)	 AG	56716-56840	GT	AGG
(AGC)	 AG	57062-57167	GT	TGG
(GGA)	 AG	58225-58391	GT	GGG
(AGA)	 AG	60260-60425	GT	AGG
(GAT)	 AG	60792-60898	GT	AGG
(AGG)	 AG	60994-61023	GT	GGG
(ACC)	 AG	61300-61439	GT	AGG
(GGA)	 AG	62085-62135	GT	AAG
(GTG)	 AG	62903-63062	GT	CGG
(ATG)	 AG	63260-63364	GT	TGG
(GCT)	 AG	63510-63698	GT	GGG
(TGG)	 AG	65248-65306	GA	AGG
-recovered Augustus_model.g13802.t1, initial, 63260, 63364
add_exon() Sorry, Augustus_model.g13802.t1 60792-60898-terminal-2 is invalid.
-recovered Augustus_model.g13802.t1, terminal, 60792, 60898
-recovered Augustus_model.g13802.t1, terminal, 65248, 65306
-recovered Augustus_model.g13802.t1, internal, 49803, 50072
-recovered Augustus_model.g13802.t1, internal, 51077, 51301
-recovered Augustus_model.g13802.t1, internal, 51484, 51561
-recovered Augustus_model.g13802.t1, internal, 51784, 51932
-recovered Augustus_model.g13802.t1, internal, 52060, 52177
-recovered Augustus_model.g13802.t1, internal, 52313, 52361
-recovered Augustus_model.g13802.t1, internal, 53712, 53771
-recovered Augustus_model.g13802.t1, internal, 55696, 55859
-recovered Augustus_model.g13802.t1, internal, 56102, 56234
-recovered Augustus_model.g13802.t1, internal, 56716, 56840
-recovered Augustus_model.g13802.t1, internal, 57062, 57167
-recovered Augustus_model.g13802.t1, internal, 58225, 58391
-recovered Augustus_model.g13802.t1, internal, 60260, 60425
-recovered Augustus_model.g13802.t1, internal, 60792, 60898
-recovered Augustus_model.g13802.t1, internal, 60994, 61023
-recovered Augustus_model.g13802.t1, internal, 61300, 61439
-recovered Augustus_model.g13802.t1, internal, 62085, 62135
-recovered Augustus_model.g13802.t1, internal, 62903, 63062
-recovered Augustus_model.g13802.t1, internal, 63260, 63364
-recovered Augustus_model.g13802.t1, internal, 63510, 63698
Valid prediction for pasa_asmbl_52265.p1
Valid prediction for snap_scaffold_8-snap.2381-T1
Valid prediction for GlimmerHMM_glimmerT_20683-T1
Valid prediction for snap_scaffold_8-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_20688-T1
Valid prediction for snap_scaffold_8-snap.2386-T1
Valid prediction for CodingQuarry_transcript_59880-T1
Valid prediction for snap_scaffold_8-snap.2375-T1
Valid prediction for CodingQuarry_transcript_59879-T1
Valid prediction for GlimmerHMM_glimmerT_20687-T1
Valid prediction for snap_scaffold_8-snap.2367-T1
Valid prediction for CodingQuarry_transcript_59875-T1
Couldn't classify 51079, 51301
Couldn't classify 63510, 63697
Sorry, prediction pasa_asmbl_52277.p1 fails validation.
(GCT)	 AA	51079-51301	GT	GGG
(AGG)	 AG	51484-51561	GT	GGG
(GTG)	 AG	51784-51932	GT	AGG
(ATA)	 AG	52060-52177	GT	TGG
(AGG)	 AG	52313-52361	GT	ACG
(TAG)	 AG	53712-53771	GT	AGG
(AGA)	 AG	54016-54018	GT	GAG
(GGC)	 AG	55696-55859	GT	AGG
(CTT)	 AG	56102-56234	GT	AGG
(CAA)	 AG	56516-56518	GT	AAG
(ATA)	 AG	56716-56840	GT	AGG
(AGC)	 AG	57062-57167	GT	TGG
(GGA)	 AG	58225-58391	GT	GGG
(AGA)	 AG	60260-60425	GT	AGG
(GAT)	 AG	60792-60898	GT	AGG
(AGG)	 AG	60994-61023	GT	GGG
(ACC)	 AG	61300-61439	GT	AGG
(GGA)	 AG	62085-62135	GT	AAG
(GTG)	 AG	62903-63062	GT	CGG
(ATG)	 AG	63260-63364	GT	TGG
(GCT)	 AG	63510-63697	GG	TGG
-recovered pasa_asmbl_52277.p1, initial, 63260, 63364
add_exon() Sorry, pasa_asmbl_52277.p1 60792-60898-terminal-2 is invalid.
-recovered pasa_asmbl_52277.p1, terminal, 60792, 60898
-recovered pasa_asmbl_52277.p1, internal, 51484, 51561
-recovered pasa_asmbl_52277.p1, internal, 51784, 51932
-recovered pasa_asmbl_52277.p1, internal, 52060, 52177
-recovered pasa_asmbl_52277.p1, internal, 52313, 52361
-recovered pasa_asmbl_52277.p1, internal, 53712, 53771
-recovered pasa_asmbl_52277.p1, internal, 54016, 54018
-recovered pasa_asmbl_52277.p1, internal, 55696, 55859
-recovered pasa_asmbl_52277.p1, internal, 56102, 56234
-recovered pasa_asmbl_52277.p1, internal, 56516, 56518
-recovered pasa_asmbl_52277.p1, internal, 56716, 56840
-recovered pasa_asmbl_52277.p1, internal, 57062, 57167
-recovered pasa_asmbl_52277.p1, internal, 58225, 58391
-recovered pasa_asmbl_52277.p1, internal, 60260, 60425
-recovered pasa_asmbl_52277.p1, internal, 60792, 60898
-recovered pasa_asmbl_52277.p1, internal, 60994, 61023
-recovered pasa_asmbl_52277.p1, internal, 61300, 61439
-recovered pasa_asmbl_52277.p1, internal, 62085, 62135
-recovered pasa_asmbl_52277.p1, internal, 62903, 63062
-recovered pasa_asmbl_52277.p1, internal, 63260, 63364

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11883, rend_intergenic: 11724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27872, rend_intergenic: 25691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35408, rend_intergenic: 30636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45038, rend_intergenic: 43447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55954, rend_intergenic: 52336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95186, rend_intergenic: 85872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103018, rend_intergenic: 95541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110361, rend_intergenic: 109253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113575, rend_intergenic: 110383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117659, rend_intergenic: 115851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132372, rend_intergenic: 119766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137196, rend_intergenic: 136986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157468, rend_intergenic: 152564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176967, rend_intergenic: 169347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182158
-exon list size: 331


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    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
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    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
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    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
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    
36.6    
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    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
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76.6    
76.9    
77.2    
77.5    
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78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
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84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
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    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
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 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11883, rend_intergenic: 11724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27872, rend_intergenic: 25691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35408, rend_intergenic: 30636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45038, rend_intergenic: 43447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55954, rend_intergenic: 52336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95186, rend_intergenic: 85872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103018, rend_intergenic: 95541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110361, rend_intergenic: 109253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113575, rend_intergenic: 110383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117659, rend_intergenic: 115851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132372, rend_intergenic: 119766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137196, rend_intergenic: 136986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157468, rend_intergenic: 152564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176967, rend_intergenic: 169347  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