-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_7139436-7372485

-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 GlimmerHMM_glimmerT_4039-T1
Couldn't classify 166302, 166700
Sorry, prediction pasa_asmbl_23246.p1 fails validation.
(ATG)	 GT	166302-166700	CT	GGC
Valid prediction for snap_scaffold_2-snap.1530-T1
Valid prediction for snap_scaffold_2-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_4057-T1
Valid prediction for pasa_asmbl_24549.p1
Valid prediction for snap_scaffold_2-snap.1564-T1
Valid prediction for snap_scaffold_2-snap.1569-T1
Valid prediction for Augustus_model.g2715.t1
Valid prediction for HiQ_model.g2713.t1
Valid prediction for CodingQuarry_transcript_28594-T1
Valid prediction for snap_scaffold_2-snap.1534-T1
Valid prediction for snap_scaffold_2-snap.1562-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1559-T1
Valid prediction for snap_scaffold_2-snap.1538-T1
Valid prediction for snap_scaffold_2-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_4047-T1
Valid prediction for snap_scaffold_2-snap.1537-T1
Valid prediction for HiQ_model.g2721.t1
Valid prediction for GlimmerHMM_glimmerT_4044-T1
Valid prediction for Augustus_model.g2717.t1
Valid prediction for Augustus_model.g2740.t1
Valid prediction for HiQ_model.g2727.t1
Valid prediction for snap_scaffold_2-snap.1552-T1
Valid prediction for Augustus_model.g2739.t1
Valid prediction for GlimmerHMM_glimmerT_4059-T1
Couldn't classify 29241, 29263
Sorry, prediction pasa_asmbl_24537.p1 fails validation.
(CTG)	 CA	29241-29263	GT	TGG
(GAG)	 AG	29362-29388	GT	CTG
(TTT)	 AG	29512-29664	GT	AGG
(AAA)	 AG	29919-29964	GT	CAG
(CCG)	 AG	32559-32648	GT	AGG
(CTG)	 AG	32800-32883	GT	AGG
(AGG)	 AG	33148-33225	AA	GAA
-recovered pasa_asmbl_24537.p1, terminal, 33148, 33225
-recovered pasa_asmbl_24537.p1, internal, 29362, 29388
-recovered pasa_asmbl_24537.p1, internal, 29512, 29664
-recovered pasa_asmbl_24537.p1, internal, 29919, 29964
-recovered pasa_asmbl_24537.p1, internal, 32559, 32648
-recovered pasa_asmbl_24537.p1, internal, 32800, 32883
Valid prediction for GlimmerHMM_glimmerT_4064-T1
Valid prediction for snap_scaffold_2-snap.1546-T1
Valid prediction for GlimmerHMM_glimmerT_4040-T1
Valid prediction for snap_scaffold_2-snap.1545-T1
Valid prediction for snap_scaffold_2-snap.1547-T1
Valid prediction for Augustus_model.g2732.t1
Valid prediction for snap_scaffold_2-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_4053-T1
Valid prediction for snap_scaffold_2-snap.1560-T1
Valid prediction for snap_scaffold_2-snap.1567-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1533-T1
Valid prediction for Augustus_model.g2731.t1
Valid prediction for Augustus_model.g2719.t1
Valid prediction for GlimmerHMM_glimmerT_4072-T1
Valid prediction for GlimmerHMM_glimmerT_4052-T1
Valid prediction for GlimmerHMM_glimmerT_4070-T1
Valid prediction for GlimmerHMM_glimmerT_4058-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g2736.t1
Valid prediction for GlimmerHMM_glimmerT_4060-T1
Valid prediction for Augustus_model.g2737.t1
Valid prediction for pasa_asmbl_24543.p1
Valid prediction for Augustus_model.g2726.t1
Valid prediction for GlimmerHMM_glimmerT_4054-T1
Valid prediction for HiQ_model.g2729.t1
Valid prediction for Augustus_model.g2725.t1
Valid prediction for Augustus_model.g2741.t1
Valid prediction for GlimmerHMM_glimmerT_4038-T1
Valid prediction for GlimmerHMM_glimmerT_4042-T1
Valid prediction for snap_scaffold_2-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_4055-T1
Valid prediction for GlimmerHMM_glimmerT_4068-T1
Valid prediction for GlimmerHMM_glimmerT_4066-T1
Valid prediction for GlimmerHMM_glimmerT_4051-T1
Valid prediction for snap_scaffold_2-snap.1555-T1
Valid prediction for snap_scaffold_2-snap.1549-T1
Valid prediction for snap_scaffold_2-snap.1565-T1
Valid prediction for snap_scaffold_2-snap.1568-T1
Valid prediction for GlimmerHMM_glimmerT_4069-T1
Valid prediction for pasa_asmbl_24552.p1

-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_2-snap.1556-T1
Valid prediction for GlimmerHMM_glimmerT_4046-T1
Valid prediction for Augustus_model.g2733.t1
Valid prediction for Augustus_model.g2743.t1
Valid prediction for Augustus_model.g2742.t1
Valid prediction for GlimmerHMM_glimmerT_4065-T1
Valid prediction for Augustus_model.g2724.t1
Valid prediction for Augustus_model.g2734.t1
Valid prediction for Augustus_model.g2716.t1
Valid prediction for Augustus_model.g2718.t1
Valid prediction for HiQ_model.g2730.t1
Valid prediction for snap_scaffold_2-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_4056-T1
Valid prediction for snap_scaffold_2-snap.1548-T1
Valid prediction for snap_scaffold_2-snap.1542-T1
Valid prediction for GlimmerHMM_glimmerT_4062-T1
Valid prediction for snap_scaffold_2-snap.1561-T1
Valid prediction for snap_scaffold_2-snap.1540-T1
Valid prediction for GlimmerHMM_glimmerT_4063-T1
Couldn't classify 94839, 94916
Sorry, prediction pasa_asmbl_23245.p1 fails validation.
(ATG)	 GA	93626-93631	GT	AGG
(GAT)	 AG	93777-94069	GT	AAG
(GGA)	 AG	94226-94454	GT	AGG
(GTC)	 AG	94563-94694	GT	AGG
(GAT)	 AG	94839-94916	AG	GGA
-recovered pasa_asmbl_23245.p1, initial, 93626, 93631
-recovered pasa_asmbl_23245.p1, internal, 93777, 94069
-recovered pasa_asmbl_23245.p1, internal, 94226, 94454
-recovered pasa_asmbl_23245.p1, internal, 94563, 94694
Valid prediction for Augustus_model.g2714.t1
Valid prediction for snap_scaffold_2-snap.1535-T1
Valid prediction for snap_scaffold_2-snap.1550-T1
Valid prediction for Augustus_model.g2723.t1
Valid prediction for GlimmerHMM_glimmerT_4073-T1
Valid prediction for snap_scaffold_2-snap.1551-T1
Valid prediction for GlimmerHMM_glimmerT_4041-T1
Valid prediction for GlimmerHMM_glimmerT_4043-T1
Valid prediction for GlimmerHMM_glimmerT_4045-T1
Valid prediction for snap_scaffold_2-snap.1554-T1
Valid prediction for snap_scaffold_2-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_4071-T1
Couldn't classify 106799, 107185
Sorry, prediction pasa_asmbl_23241.p1 fails validation.
(AAG)	 GG	106799-107185	AA	AAA
Valid prediction for Augustus_model.g2720.t1
Valid prediction for GlimmerHMM_glimmerT_4048-T1
Valid prediction for GlimmerHMM_glimmerT_4050-T1
Valid prediction for GlimmerHMM_glimmerT_4061-T1
Couldn't classify 105681, 105799
Couldn't classify 105904, 106630
Sorry, prediction pasa_asmbl_23242.p1 fails validation.
(CCA)	 CT	105681-105799	GT	AGG
(AGT)	 AG	105904-106630	GA	TGG
Couldn't classify 95142, 95186
Sorry, prediction pasa_asmbl_23244.p1 fails validation.
(GTC)	 CC	95142-95186	GT	AGG
(ATC)	 AG	95320-95571	GT	TGG
(ATG)	 AG	95731-95905	GT	CCG
(TCT)	 AG	96445-96465	GT	CCG
(CTC)	 AG	96562-96740	CA	AAC
-recovered pasa_asmbl_23244.p1, initial, 95731, 95905
-recovered pasa_asmbl_23244.p1, terminal, 96562, 96740
-recovered pasa_asmbl_23244.p1, internal, 95320, 95571
-recovered pasa_asmbl_23244.p1, internal, 95731, 95905
-recovered pasa_asmbl_23244.p1, internal, 96445, 96465
Valid prediction for GlimmerHMM_glimmerT_4049-T1
Valid prediction for snap_scaffold_2-snap.1539-T1
Valid prediction for snap_scaffold_2-snap.1541-T1
Valid prediction for Augustus_model.g2722.t1
Valid prediction for Augustus_model.g2738.t1
Valid prediction for Augustus_model.g2728.t1
Valid prediction for GlimmerHMM_glimmerT_4067-T1
Valid prediction for snap_scaffold_2-snap.1553-T1
Valid prediction for snap_scaffold_2-snap.1543-T1
Valid prediction for snap_scaffold_2-snap.1557-T1
Valid prediction for snap_scaffold_2-snap.1558-T1
Valid prediction for Augustus_model.g2735.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 67247, rend_intergenic: 65728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233050
-exon list size: 364


building trellis

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1.9    
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3.6    
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4.6    
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5.7    
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6.8    
7.1    
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10.7    
10.9    
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11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
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13.9    
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14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
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16.4    
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16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
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24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
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    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 67247, rend_intergenic: 65728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support