-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_2425467-2612363

-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_39895-T1
Valid prediction for CodingQuarry_transcript_21890-T1
Valid prediction for GlimmerHMM_glimmerT_39919-T1
Valid prediction for snap_scaffold_17-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_39902-T1
Valid prediction for HiQ_model.g26566.t1
Valid prediction for GlimmerHMM_glimmerT_39921-T1
Valid prediction for GlimmerHMM_glimmerT_39922-T1
Couldn't classify 50537, 50656
Couldn't classify 52969, 52985
Sorry, prediction pasa_asmbl_18656.p1 fails validation.
(AGC)	 CC	50537-50656	GT	AGG
(TGT)	 AG	50747-50835	GT	GGG
(CTT)	 AG	50946-51090	GT	AGG
(GCG)	 AG	51344-51498	GT	TGG
(GGA)	 AG	51592-51680	GT	GCG
(TGG)	 AG	51817-51947	GT	AGG
(TGT)	 AG	52243-52377	GT	AGG
(GCT)	 AG	52610-52696	GT	GGG
(TTG)	 AG	52809-52875	GT	ACG
(GTG)	 AG	52969-52985	GA	CAG
-recovered pasa_asmbl_18656.p1, internal, 50747, 50835
-recovered pasa_asmbl_18656.p1, internal, 50946, 51090
-recovered pasa_asmbl_18656.p1, internal, 51344, 51498
-recovered pasa_asmbl_18656.p1, internal, 51592, 51680
-recovered pasa_asmbl_18656.p1, internal, 51817, 51947
-recovered pasa_asmbl_18656.p1, internal, 52243, 52377
-recovered pasa_asmbl_18656.p1, internal, 52610, 52696
-recovered pasa_asmbl_18656.p1, internal, 52809, 52875
Valid prediction for snap_scaffold_17-snap.527-T1
Valid prediction for snap_scaffold_17-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_39903-T1
Valid prediction for snap_scaffold_17-snap.541-T1
Valid prediction for CodingQuarry_transcript_21900-T1
Valid prediction for snap_scaffold_17-snap.542-T1
Valid prediction for snap_scaffold_17-snap.536-T1
Valid prediction for Augustus_model.g26571.t1
Valid prediction for Augustus_model.g26569.t1
Valid prediction for GlimmerHMM_glimmerT_39899-T1
Valid prediction for HiQ_model.g26568.t1
Valid prediction for pasa_asmbl_18655.p1
Valid prediction for GlimmerHMM_glimmerT_39909-T1
Valid prediction for GlimmerHMM_glimmerT_39918-T1
Couldn't classify 147677, 147736
Sorry, prediction pasa_asmbl_18667.p1 fails validation.
(ATG)	 CA	144105-144109	GT	AGG
(AGG)	 AG	144647-144706	GT	GGG
(GTA)	 AG	144867-144909	GT	TGG
(TGT)	 AG	145116-145220	GT	AGG
(TCT)	 AG	145333-145410	GT	TGG
(CAA)	 AG	145508-145610	GT	ATG
(TGG)	 AG	145739-145804	GT	AGG
(TTC)	 AG	145952-146068	GT	CTG
(TGG)	 AG	146577-146655	GT	ACG
(GGT)	 AG	146844-146931	GT	TGG
(GGT)	 AG	147203-147264	GT	AGG
(ACG)	 AG	147381-147495	GT	AGG
(GAT)	 AG	147677-147736	AA	GGA
-recovered pasa_asmbl_18667.p1, initial, 144105, 144109
-recovered pasa_asmbl_18667.p1, internal, 144647, 144706
-recovered pasa_asmbl_18667.p1, internal, 144867, 144909
-recovered pasa_asmbl_18667.p1, internal, 145116, 145220
-recovered pasa_asmbl_18667.p1, internal, 145333, 145410
-recovered pasa_asmbl_18667.p1, internal, 145508, 145610
-recovered pasa_asmbl_18667.p1, internal, 145739, 145804
-recovered pasa_asmbl_18667.p1, internal, 145952, 146068
-recovered pasa_asmbl_18667.p1, internal, 146577, 146655
-recovered pasa_asmbl_18667.p1, internal, 146844, 146931
-recovered pasa_asmbl_18667.p1, internal, 147203, 147264
-recovered pasa_asmbl_18667.p1, internal, 147381, 147495
Couldn't classify 59986, 60095
Sorry, prediction pasa_asmbl_18659.p1 fails validation.
(AAA)	 CC	59986-60095	GT	CGG
(CTT)	 AG	60536-60612	GT	AGG
(GTG)	 AG	60825-61016	GT	AGG
(TGG)	 AG	62240-62316	TC	AAT
-recovered pasa_asmbl_18659.p1, terminal, 62240, 62316
-recovered pasa_asmbl_18659.p1, internal, 60536, 60612
-recovered pasa_asmbl_18659.p1, internal, 60825, 61016
Valid prediction for HiQ_model.g26584.t1
Valid prediction for snap_scaffold_17-snap.524-T1
Valid prediction for HiQ_model.g26575.t1
Valid prediction for pasa_asmbl_18652.p1
Valid prediction for GlimmerHMM_glimmerT_39896-T1
Valid prediction for GlimmerHMM_glimmerT_39913-T1
Couldn't classify 55328, 56314
Sorry, prediction pasa_asmbl_18658.p1 fails validation.
(ACT)	 GG	55328-56314	AG	GAA
Valid prediction for snap_scaffold_17-snap.518-T1
Valid prediction for pasa_asmbl_18660.p1
Valid prediction for GlimmerHMM_glimmerT_39912-T1
Valid prediction for GlimmerHMM_glimmerT_39897-T1
Valid prediction for CodingQuarry_transcript_21886-T1
Valid prediction for GlimmerHMM_glimmerT_39900-T1
Valid prediction for snap_scaffold_17-snap.519-T1
Valid prediction for snap_scaffold_17-snap.520-T1
Valid prediction for snap_scaffold_17-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_39924-T1
Valid prediction for pasa_asmbl_18662.p1
Valid prediction for CodingQuarry_transcript_21899-T1
Valid prediction for Augustus_model.g26567.t1
Valid prediction for HiQ_model.g26585.t1
Couldn't classify 53040, 53114
Couldn't classify 54897, 55135
Sorry, prediction pasa_asmbl_18657.p1 fails validation.
(TTA)	 TG	53040-53114	GT	AGG
(ACG)	 AG	53327-53505	GT	AAG
(TTT)	 AG	54086-54137	GT	AGG
(ATG)	 AG	54364-54417	GT	AGG
(GAG)	 AG	54591-54714	GT	AGG
(AAG)	 AG	54897-55135	GA	GGG
-recovered pasa_asmbl_18657.p1, initial, 54364, 54417
-recovered pasa_asmbl_18657.p1, terminal, 54591, 54714
-recovered pasa_asmbl_18657.p1, internal, 53327, 53505
-recovered pasa_asmbl_18657.p1, internal, 54086, 54137
-recovered pasa_asmbl_18657.p1, internal, 54364, 54417
-recovered pasa_asmbl_18657.p1, internal, 54591, 54714
Valid prediction for snap_scaffold_17-snap.517-T1
Valid prediction for snap_scaffold_17-snap.548-T1
Valid prediction for Augustus_model.g26572.t1
Valid prediction for snap_scaffold_17-snap.526-T1
Valid prediction for snap_scaffold_17-snap.521-T1
Valid prediction for pasa_asmbl_18661.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_17-snap.522-T1
Valid prediction for Augustus_model.g26565.t1
Valid prediction for Augustus_model.g26579.t1
Valid prediction for GlimmerHMM_glimmerT_39925-T1
Valid prediction for snap_scaffold_17-snap.529-T1
Valid prediction for HiQ_model.g26578.t1
Valid prediction for snap_scaffold_17-snap.534-T1
Valid prediction for pasa_asmbl_17751.p1
Valid prediction for GlimmerHMM_glimmerT_39923-T1
Valid prediction for GlimmerHMM_glimmerT_39911-T1
Valid prediction for snap_scaffold_17-snap.525-T1
Valid prediction for CodingQuarry_transcript_21888-T1
Valid prediction for GlimmerHMM_glimmerT_39915-T1
Valid prediction for GlimmerHMM_glimmerT_39914-T1
Valid prediction for CodingQuarry_transcript_21897-T1
Valid prediction for GlimmerHMM_glimmerT_39908-T1
Valid prediction for snap_scaffold_17-snap.545-T1
Valid prediction for snap_scaffold_17-snap.530-T1
Valid prediction for Augustus_model.g26586.t1
Valid prediction for HiQ_model.g26583.t1
Valid prediction for pasa_asmbl_17752.p1
Couldn't classify 57376, 57577
Sorry, prediction pasa_asmbl_17763.p1 fails validation.
(TTA)	 GG	57376-57577	GT	GCG
(TGT)	 AG	57980-58210	GT	CAG
(CAA)	 AG	58979-59083	GT	CTG
(GGT)	 AG	59442-59495	GT	AGG
(GGC)	 AG	59611-59794	GT	AGG
(GTT)	 AG	60044-60212	GT	AGG
(GTG)	 AG	60983-61121	GT	CAG
(GTC)	 AG	61257-61468	CT	GAC
-recovered pasa_asmbl_17763.p1, terminal, 61257, 61468
-recovered pasa_asmbl_17763.p1, internal, 57980, 58210
-recovered pasa_asmbl_17763.p1, internal, 58979, 59083
-recovered pasa_asmbl_17763.p1, internal, 59442, 59495
-recovered pasa_asmbl_17763.p1, internal, 59611, 59794
-recovered pasa_asmbl_17763.p1, internal, 60044, 60212
-recovered pasa_asmbl_17763.p1, internal, 60983, 61121
Valid prediction for snap_scaffold_17-snap.516-T1
Valid prediction for HiQ_model.g26576.t1
Valid prediction for GlimmerHMM_glimmerT_39906-T1
Valid prediction for HiQ_model.g26580.t1
Valid prediction for GlimmerHMM_glimmerT_39898-T1
Valid prediction for snap_scaffold_17-snap.537-T1
Valid prediction for CodingQuarry_transcript_21892-T1
Valid prediction for GlimmerHMM_glimmerT_39916-T1
Valid prediction for snap_scaffold_17-snap.535-T1
Valid prediction for snap_scaffold_17-snap.523-T1
Valid prediction for Augustus_model.g26570.t1
Valid prediction for GlimmerHMM_glimmerT_39904-T1
Valid prediction for pasa_asmbl_17756.p1
Valid prediction for snap_scaffold_17-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_39910-T1
Valid prediction for CodingQuarry_transcript_21893-T1
Valid prediction for GlimmerHMM_glimmerT_39894-T1
Valid prediction for CodingQuarry_transcript_21894-T1
Valid prediction for snap_scaffold_17-snap.531-T1
Valid prediction for Augustus_model.g26582.t1
Valid prediction for snap_scaffold_17-snap.547-T1
Couldn't classify 154259, 155677
Sorry, prediction pasa_asmbl_17748.p1 fails validation.
(CAA)	 CA	154259-155677	GT	AGG
(ATG)	 AG	156174-156194	CT	AAC
-recovered pasa_asmbl_17748.p1, terminal, 156174, 156194
Couldn't classify 112426, 112527
Couldn't classify 113786, 113861
Sorry, prediction CodingQuarry_transcript_21889-T1 fails validation.
(ATG)	 AG	111365-111466	GT	TGG
(GAG)	 AG	111709-111882	GT	AGG
(ACG)	 AG	112012-112184	GT	AAG
(ACT)	 AG	112426-112527	CC	GAC
(GAC)	 AA	113786-113861	GT	AGG
(GTT)	 AG	113984-114149	GT	AGG
(TTG)	 AG	114354-114469	GT	AGG
(AAG)	 AG	114902-115119	GT	TGG
(GTA)	 AG	115271-115346	AC	AAA
-recovered CodingQuarry_transcript_21889-T1, initial, 111365, 111466
add_exon() Sorry, CodingQuarry_transcript_21889-T1 113984-114149-terminal-3 is invalid.
-recovered CodingQuarry_transcript_21889-T1, terminal, 113984, 114149
-recovered CodingQuarry_transcript_21889-T1, terminal, 115271, 115346
-recovered CodingQuarry_transcript_21889-T1, internal, 111365, 111466
-recovered CodingQuarry_transcript_21889-T1, internal, 111709, 111882
-recovered CodingQuarry_transcript_21889-T1, internal, 112012, 112184
-recovered CodingQuarry_transcript_21889-T1, internal, 113984, 114149
-recovered CodingQuarry_transcript_21889-T1, internal, 114354, 114469
-recovered CodingQuarry_transcript_21889-T1, internal, 114902, 115119
Valid prediction for GlimmerHMM_glimmerT_39905-T1
Valid prediction for CodingQuarry_transcript_21896-T1
Valid prediction for Augustus_model.g26573.t1
Valid prediction for CodingQuarry_transcript_21898-T1
Valid prediction for snap_scaffold_17-snap.539-T1
Couldn't classify 29313, 29465
Sorry, prediction pasa_asmbl_17768.p1 fails validation.
(GAA)	 CT	29313-29465	GT	TGG
(GAC)	 AG	30266-30319	GT	AGG
(GTC)	 AG	30448-30996	GA	GAG
-recovered pasa_asmbl_17768.p1, terminal, 30448, 30996
-recovered pasa_asmbl_17768.p1, internal, 30266, 30319
Valid prediction for pasa_asmbl_17750.p1
Valid prediction for HiQ_model.g26574.t1
Valid prediction for snap_scaffold_17-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_39920-T1
Couldn't classify 121276, 121911
Sorry, prediction pasa_asmbl_17749.p1 fails validation.
(CCT)	 CA	121276-121911	GC	AGG
Valid prediction for snap_scaffold_17-snap.544-T1
Valid prediction for snap_scaffold_17-snap.528-T1
Valid prediction for HiQ_model.g26577.t1
Valid prediction for Augustus_model.g26587.t1
Valid prediction for snap_scaffold_17-snap.540-T1
Couldn't classify 49015, 49136
Sorry, prediction pasa_asmbl_17767.p1 fails validation.
(CCA)	 CG	49015-49136	GT	AGG
(GGA)	 AG	49958-50004	GT	TGG
(AGC)	 AG	50135-50253	GT	AGG
(GAG)	 AG	50780-50887	CT	AAC
-recovered pasa_asmbl_17767.p1, terminal, 50780, 50887
-recovered pasa_asmbl_17767.p1, internal, 49958, 50004
-recovered pasa_asmbl_17767.p1, internal, 50135, 50253
Valid prediction for pasa_asmbl_17754.p1
Valid prediction for GlimmerHMM_glimmerT_39917-T1
Valid prediction for pasa_asmbl_17755.p1
Valid prediction for CodingQuarry_transcript_21891-T1
Valid prediction for GlimmerHMM_glimmerT_39901-T1
Valid prediction for GlimmerHMM_glimmerT_39907-T1
Valid prediction for Augustus_model.g26581.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56314, rend_intergenic: 46585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130791, rend_intergenic: 127266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186897
-exon list size: 356


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.7    
8.9    
9.2    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.1    
91.3    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 56314, rend_intergenic: 46585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130791, rend_intergenic: 127266  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