-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_18729517-18916243

-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.g9384.t1
Valid prediction for GeneMark_model.23565_t
Valid prediction for Augustus_model.g9373.t1
Valid prediction for CodingQuarry_transcript_52343-T1
Valid prediction for snap_scaffold_5-snap.3549-T1
Valid prediction for snap_scaffold_5-snap.3544-T1
Valid prediction for snap_scaffold_5-snap.3567-T1
Valid prediction for GlimmerHMM_glimmerT_14035-T1
Valid prediction for GeneMark_model.23555_t
Valid prediction for Augustus_model.g9375.t1
Valid prediction for snap_scaffold_5-snap.3564-T1
Valid prediction for GeneMark_model.23563_t
Valid prediction for GlimmerHMM_glimmerT_14052-T1
Valid prediction for GeneMark_model.23561_t
Valid prediction for GeneMark_model.23562_t
Valid prediction for GlimmerHMM_glimmerT_14034-T1
Valid prediction for GlimmerHMM_glimmerT_14044-T1
Valid prediction for snap_scaffold_5-snap.3551-T1
Valid prediction for GlimmerHMM_glimmerT_14051-T1
Valid prediction for GlimmerHMM_glimmerT_14049-T1
Valid prediction for GlimmerHMM_glimmerT_14040-T1
Valid prediction for GlimmerHMM_glimmerT_14031-T1
Valid prediction for GeneMark_model.23545_t
Valid prediction for GlimmerHMM_glimmerT_14046-T1
Valid prediction for snap_scaffold_5-snap.3537-T1
Valid prediction for GeneMark_model.23556_t
Valid prediction for snap_scaffold_5-snap.3541-T1
Valid prediction for snap_scaffold_5-snap.3552-T1
Valid prediction for GlimmerHMM_glimmerT_14050-T1
Couldn't classify 119981, 120430
Sorry, prediction pasa_asmbl_45094.p1 fails validation.
(TCC)	 GC	119981-120430	AA	GCA
Valid prediction for snap_scaffold_5-snap.3550-T1
Valid prediction for HiQ_model.g9379.t1
Valid prediction for pasa_asmbl_44934.p1
Valid prediction for GeneMark_model.23557_t
Valid prediction for GlimmerHMM_glimmerT_14047-T1
Valid prediction for GlimmerHMM_glimmerT_14032-T1
Valid prediction for HiQ_model.g9374.t1
Valid prediction for GeneMark_model.23553_t
Valid prediction for snap_scaffold_5-snap.3540-T1
Valid prediction for HiQ_model.g9372.t1
Valid prediction for HiQ_model.g9369.t1
Valid prediction for GeneMark_model.23552_t
Valid prediction for GlimmerHMM_glimmerT_14038-T1
Couldn't classify 94065, 94101
Sorry, prediction pasa_asmbl_44947.p1 fails validation.
(CTA)	 GC	94065-94101	GT	AGG
(TTC)	 AG	94733-94787	GT	AAG
(GCA)	 AG	95791-95921	GT	AGG
(GTG)	 AG	96045-96153	GT	CAG
(GAT)	 AG	96251-96338	GT	CTG
(GTC)	 AG	96463-96550	GT	TCG
(ACG)	 AG	97179-97285	GT	AGG
(GTT)	 AG	97518-97683	GT	AGG
(TGA)	 AG	97760-97785	GT	AGG
(GCC)	 AG	97894-98134	GT	TGG
(AGT)	 AG	98476-98877	GT	CGG
(CTA)	 AG	99317-99417	GT	TGG
(CAC)	 AG	99786-99893	GT	TGG
(GCG)	 AG	100034-100103	GT	AGG
(ACC)	 AG	102042-102134	GT	AGG
(GTG)	 AG	102423-102607	TG	AGT
-recovered pasa_asmbl_44947.p1, terminal, 102423, 102607
-recovered pasa_asmbl_44947.p1, internal, 94733, 94787
-recovered pasa_asmbl_44947.p1, internal, 95791, 95921
-recovered pasa_asmbl_44947.p1, internal, 96045, 96153
-recovered pasa_asmbl_44947.p1, internal, 96251, 96338
-recovered pasa_asmbl_44947.p1, internal, 96463, 96550
-recovered pasa_asmbl_44947.p1, internal, 97179, 97285
-recovered pasa_asmbl_44947.p1, internal, 97518, 97683
-recovered pasa_asmbl_44947.p1, internal, 97760, 97785
-recovered pasa_asmbl_44947.p1, internal, 97894, 98134
-recovered pasa_asmbl_44947.p1, internal, 98476, 98877
-recovered pasa_asmbl_44947.p1, internal, 99317, 99417
-recovered pasa_asmbl_44947.p1, internal, 99786, 99893
-recovered pasa_asmbl_44947.p1, internal, 100034, 100103
-recovered pasa_asmbl_44947.p1, internal, 102042, 102134
Couldn't classify 101454, 101559
Sorry, prediction pasa_asmbl_44948.p1 fails validation.
(CTG)	 CC	101454-101559	GT	AGG
(ACC)	 AG	102042-102134	GT	AGG
(GTG)	 AG	102423-102607	TG	AGT
-recovered pasa_asmbl_44948.p1, terminal, 102423, 102607
-recovered pasa_asmbl_44948.p1, internal, 102042, 102134
Valid prediction for snap_scaffold_5-snap.3539-T1
Valid prediction for GlimmerHMM_glimmerT_14041-T1
Valid prediction for CodingQuarry_transcript_52342-T1
Valid prediction for GeneMark_model.23547_t
Valid prediction for GeneMark_model.23551_t
Valid prediction for snap_scaffold_5-snap.3557-T1
Valid prediction for snap_scaffold_5-snap.3561-T1
Valid prediction for Augustus_model.g9386.t1
Valid prediction for snap_scaffold_5-snap.3546-T1
Couldn't classify 46696, 47085
Sorry, prediction pasa_asmbl_44936.p1 fails validation.
(TTC)	 CT	46696-47085	GT	AGG
(GGC)	 AG	47229-47467	GT	AGG
(GCT)	 AG	47753-47922	GT	GGG
(AGT)	 AG	48368-48585	GT	AGG
(GAA)	 AG	48701-48865	GT	AGG
(GTG)	 AG	48985-49092	GT	AGG
(CCG)	 AG	49342-49481	GT	AAG
(GTA)	 AG	49625-49757	GT	AGG
(GTG)	 AG	50030-50347	GC	GAG
-recovered pasa_asmbl_44936.p1, terminal, 50030, 50347
-recovered pasa_asmbl_44936.p1, internal, 47229, 47467
-recovered pasa_asmbl_44936.p1, internal, 47753, 47922
-recovered pasa_asmbl_44936.p1, internal, 48368, 48585
-recovered pasa_asmbl_44936.p1, internal, 48701, 48865
-recovered pasa_asmbl_44936.p1, internal, 48985, 49092
-recovered pasa_asmbl_44936.p1, internal, 49342, 49481
-recovered pasa_asmbl_44936.p1, internal, 49625, 49757
-recovered pasa_asmbl_44936.p1, internal, 50030, 50347
Couldn't classify 87908, 88018
Sorry, prediction pasa_asmbl_44944.p1 fails validation.
(TAC)	 GC	87908-88018	GT	AGG
(TAC)	 AG	88170-88199	GT	GAG
(GAC)	 AG	88639-88686	GT	AGG
(ATC)	 AG	88855-88969	GT	GGG
(TTG)	 AG	89101-89172	GT	CCG
(ACA)	 AG	90083-90162	GT	CTG
(GCC)	 AG	91531-91609	GT	AGG
(CGG)	 AG	91749-91922	GT	ACG
(GGT)	 AG	92065-92129	GA	GAG
-recovered pasa_asmbl_44944.p1, terminal, 92065, 92129
-recovered pasa_asmbl_44944.p1, internal, 88170, 88199
-recovered pasa_asmbl_44944.p1, internal, 88639, 88686
-recovered pasa_asmbl_44944.p1, internal, 88855, 88969
-recovered pasa_asmbl_44944.p1, internal, 89101, 89172
-recovered pasa_asmbl_44944.p1, internal, 90083, 90162
-recovered pasa_asmbl_44944.p1, internal, 91531, 91609
-recovered pasa_asmbl_44944.p1, internal, 91749, 91922
Valid prediction for HiQ_model.g9380.t1
Valid prediction for snap_scaffold_5-snap.3565-T1
Valid prediction for snap_scaffold_5-snap.3556-T1
Valid prediction for GeneMark_model.23566_t
Valid prediction for GeneMark_model.23548_t
Valid prediction for GlimmerHMM_glimmerT_14045-T1
Valid prediction for GlimmerHMM_glimmerT_14053-T1
Valid prediction for GlimmerHMM_glimmerT_14030-T1
Valid prediction for Augustus_model.g9378.t1
Valid prediction for Augustus_model.g9367.t1
Valid prediction for GlimmerHMM_glimmerT_14054-T1
Valid prediction for snap_scaffold_5-snap.3553-T1
Valid prediction for GeneMark_model.23544_t
Valid prediction for GlimmerHMM_glimmerT_14039-T1
Valid prediction for snap_scaffold_5-snap.3566-T1
Valid prediction for GlimmerHMM_glimmerT_14033-T1
Valid prediction for Augustus_model.g9382.t1
Valid prediction for GeneMark_model.23550_t
Valid prediction for Augustus_model.g9385.t1
Couldn't classify 79390, 79452
Sorry, prediction pasa_asmbl_44941.p1 fails validation.
(TGT)	 CA	79390-79452	GT	AGG
(AGA)	 AG	79546-79724	GT	AAG
(ACT)	 AG	80113-80278	GT	AGG
(AGA)	 AG	80396-80464	AA	AGA
-recovered pasa_asmbl_44941.p1, terminal, 80396, 80464
-recovered pasa_asmbl_44941.p1, internal, 79546, 79724
-recovered pasa_asmbl_44941.p1, internal, 80113, 80278
Couldn't classify 84438, 84485
Sorry, prediction pasa_asmbl_44943.p1 fails validation.
(ATG)	 GA	82045-82163	GT	TGG
(CTC)	 AG	84116-84245	GT	ATG
(GTG)	 AG	84438-84485	TT	AGT
-recovered pasa_asmbl_44943.p1, initial, 82045, 82163
-recovered pasa_asmbl_44943.p1, internal, 84116, 84245
Valid prediction for GlimmerHMM_glimmerT_14043-T1
Valid prediction for Augustus_model.g9383.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_14037-T1
Valid prediction for GeneMark_model.23554_t
Valid prediction for snap_scaffold_5-snap.3555-T1
Valid prediction for snap_scaffold_5-snap.3563-T1
Valid prediction for GeneMark_model.23564_t
Valid prediction for snap_scaffold_5-snap.3558-T1
Couldn't classify 158160, 158161
Sorry, prediction CodingQuarry_transcript_52341-T1 fails validation.
(ATG)	 AA	157501-157532	GT	AGG
(CTA)	 AG	157846-157967	GT	TTG
(GAT)	 AG	158160-158161	TC	GAT
-recovered CodingQuarry_transcript_52341-T1, initial, 157501, 157532
-recovered CodingQuarry_transcript_52341-T1, internal, 157846, 157967
Valid prediction for GlimmerHMM_glimmerT_14042-T1
Valid prediction for Augustus_model.g9381.t1
Valid prediction for GeneMark_model.23543_t
Valid prediction for snap_scaffold_5-snap.3542-T1
Valid prediction for GeneMark_model.23549_t
Valid prediction for snap_scaffold_5-snap.3548-T1
Valid prediction for snap_scaffold_5-snap.3545-T1
Valid prediction for snap_scaffold_5-snap.3559-T1
Valid prediction for Augustus_model.g9377.t1
Valid prediction for snap_scaffold_5-snap.3547-T1
Valid prediction for snap_scaffold_5-snap.3554-T1
Valid prediction for HiQ_model.g9371.t1
Valid prediction for snap_scaffold_5-snap.3560-T1
Valid prediction for snap_scaffold_5-snap.3538-T1
Valid prediction for GeneMark_model.23559_t
Valid prediction for snap_scaffold_5-snap.3562-T1
Valid prediction for GlimmerHMM_glimmerT_14036-T1
Valid prediction for Augustus_model.g9370.t1
Valid prediction for GlimmerHMM_glimmerT_14048-T1
Valid prediction for snap_scaffold_5-snap.3543-T1
Valid prediction for Augustus_model.g9376.t1
Valid prediction for HiQ_model.g9368.t1
Valid prediction for GeneMark_model.23560_t
Valid prediction for GeneMark_model.23546_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6534, rend_intergenic: 5646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10731, rend_intergenic: 6793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121313, rend_intergenic: 119337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186727
-exon list size: 451


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
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3.5    
3.8    
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4.6    
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7.9    
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8.6    
8.8    
9.1    
9.3    
9.5    
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10.8    
11.0    
11.3    
11.5    
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11.9    
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12.4    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
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14.3    
14.6    
14.8    
15.0    
15.2    
15.5    
15.7    
15.9    
16.1    
16.3    
16.6    
16.8    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.4    
21.6    
21.9    
22.1    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.8    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.3    
67.5    
67.8    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.4    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 6534, rend_intergenic: 5646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10731, rend_intergenic: 6793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121313, rend_intergenic: 119337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support