-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_5582001-5733982

-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_15-snap.1234-T1
Valid prediction for snap_scaffold_15-snap.1228-T1
Valid prediction for snap_scaffold_15-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_36209-T1
Valid prediction for GlimmerHMM_glimmerT_36224-T1
Couldn't classify 76699, 77037
Sorry, prediction pasa_asmbl_15218.p1 fails validation.
(AGC)	 GT	76699-77037	GT	AGG
(TTC)	 AG	77396-77575	GT	GGG
(TTC)	 AG	78002-78055	GA	GAG
-recovered pasa_asmbl_15218.p1, terminal, 78002, 78055
-recovered pasa_asmbl_15218.p1, internal, 77396, 77575
Valid prediction for GlimmerHMM_glimmerT_36218-T1
Valid prediction for Augustus_model.g24143.t1
Valid prediction for GlimmerHMM_glimmerT_36222-T1
Valid prediction for GlimmerHMM_glimmerT_36225-T1
Valid prediction for snap_scaffold_15-snap.1220-T1
Couldn't classify 122061, 122118
Couldn't classify 123386, 123466
Sorry, prediction pasa_asmbl_15222.p2 fails validation.
(TGC)	 AG	122061-122118	GT	AGG
(TGT)	 AG	122256-122392	GT	GGG
(GTG)	 AG	122763-122902	GT	AGG
(GGA)	 AG	122996-123077	GT	GAG
(GTG)	 AG	123386-123466	AA	ACA
-recovered pasa_asmbl_15222.p2, internal, 122061, 122118
-recovered pasa_asmbl_15222.p2, internal, 122256, 122392
-recovered pasa_asmbl_15222.p2, internal, 122763, 122902
-recovered pasa_asmbl_15222.p2, internal, 122996, 123077
Valid prediction for Augustus_model.g24135.t1
Valid prediction for GlimmerHMM_glimmerT_36220-T1
Valid prediction for GlimmerHMM_glimmerT_36211-T1
Valid prediction for GlimmerHMM_glimmerT_36228-T1
Valid prediction for snap_scaffold_15-snap.1215-T1
Couldn't classify 127992, 128088
Sorry, prediction pasa_asmbl_15224.p1 fails validation.
(CGA)	 GC	127992-128088	GT	ACG
(GAT)	 AG	128202-128362	GT	AGG
(GAC)	 AG	131356-131487	AT	GAA
-recovered pasa_asmbl_15224.p1, terminal, 131356, 131487
-recovered pasa_asmbl_15224.p1, internal, 128202, 128362
Valid prediction for snap_scaffold_15-snap.1231-T1
Couldn't classify 112500, 112638
Couldn't classify 113599, 113641
Sorry, prediction pasa_asmbl_15220.p1 fails validation.
(GAG)	 AG	112500-112638	GT	TGG
(GTA)	 AG	112846-112955	GT	CTG
(GAG)	 AG	113085-113164	GT	TGG
(TAC)	 AG	113599-113641	CA	GCC
-recovered pasa_asmbl_15220.p1, internal, 112500, 112638
-recovered pasa_asmbl_15220.p1, internal, 112846, 112955
-recovered pasa_asmbl_15220.p1, internal, 113085, 113164
Valid prediction for snap_scaffold_15-snap.1214-T1
Valid prediction for snap_scaffold_15-snap.1244-T1
Couldn't classify 114507, 114620
Couldn't classify 119447, 119514
Sorry, prediction pasa_asmbl_15221.p1 fails validation.
(CAG)	 AG	114507-114620	GT	AGG
(GAC)	 AG	114733-114975	GT	AGG
(CTG)	 AG	115178-115288	GT	AGG
(CAG)	 AG	115374-115621	GT	AGG
(CCA)	 AG	116354-116459	GT	AGG
(CTG)	 AG	117742-117866	GT	TGG
(GGT)	 AG	118576-118681	GT	CGG
(GAC)	 AG	118928-119076	GT	TGG
(TAA)	 AG	119222-119313	GT	GGG
(GGG)	 AG	119447-119514	CA	ACC
-recovered pasa_asmbl_15221.p1, internal, 114507, 114620
-recovered pasa_asmbl_15221.p1, internal, 114733, 114975
-recovered pasa_asmbl_15221.p1, internal, 115178, 115288
-recovered pasa_asmbl_15221.p1, internal, 115374, 115621
-recovered pasa_asmbl_15221.p1, internal, 116354, 116459
-recovered pasa_asmbl_15221.p1, internal, 117742, 117866
-recovered pasa_asmbl_15221.p1, internal, 118576, 118681
-recovered pasa_asmbl_15221.p1, internal, 118928, 119076
-recovered pasa_asmbl_15221.p1, internal, 119222, 119313
Valid prediction for GlimmerHMM_glimmerT_36212-T1
Valid prediction for snap_scaffold_15-snap.1247-T1
Valid prediction for snap_scaffold_15-snap.1236-T1
Valid prediction for snap_scaffold_15-snap.1217-T1
Valid prediction for snap_scaffold_15-snap.1210-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g24142.t1
Couldn't classify 125622, 125693
Couldn't classify 127397, 127505
Sorry, prediction pasa_asmbl_15223.p1 fails validation.
(TAC)	 TG	125622-125693	GT	AGG
(GTG)	 AG	125825-125909	GT	AGG
(AGG)	 AG	126718-126841	GT	AGG
(AGA)	 AG	127397-127505	CT	ACC
-recovered pasa_asmbl_15223.p1, internal, 125825, 125909
-recovered pasa_asmbl_15223.p1, internal, 126718, 126841
Valid prediction for snap_scaffold_15-snap.1227-T1
Valid prediction for HiQ_model.g24140.t1
Valid prediction for GlimmerHMM_glimmerT_36207-T1
Valid prediction for GlimmerHMM_glimmerT_36208-T1
Valid prediction for snap_scaffold_15-snap.1222-T1
Valid prediction for snap_scaffold_15-snap.1246-T1
Valid prediction for pasa_asmbl_15215.p1
Valid prediction for CodingQuarry_transcript_18013-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 snap_scaffold_15-snap.1211-T1
Valid prediction for snap_scaffold_15-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_36221-T1
Valid prediction for snap_scaffold_15-snap.1230-T1
Couldn't classify 107466, 107607
Sorry, prediction pasa_asmbl_14226.p1 fails validation.
(AGT)	 AG	107466-107607	GT	CGG
(ATG)	 AG	107804-108012	CC	AAC
-recovered pasa_asmbl_14226.p1, terminal, 107804, 108012
-recovered pasa_asmbl_14226.p1, internal, 107466, 107607
Valid prediction for GlimmerHMM_glimmerT_36227-T1
Valid prediction for GlimmerHMM_glimmerT_36215-T1
Valid prediction for Augustus_model.g24139.t1
Valid prediction for snap_scaffold_15-snap.1216-T1
Valid prediction for snap_scaffold_15-snap.1242-T1
Valid prediction for snap_scaffold_15-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_36210-T1
Valid prediction for snap_scaffold_15-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_36216-T1
Valid prediction for GlimmerHMM_glimmerT_36226-T1
Valid prediction for GlimmerHMM_glimmerT_36223-T1
Valid prediction for snap_scaffold_15-snap.1219-T1
Valid prediction for Augustus_model.g24145.t1
Valid prediction for snap_scaffold_15-snap.1235-T1
Valid prediction for snap_scaffold_15-snap.1229-T1
Valid prediction for snap_scaffold_15-snap.1221-T1
Valid prediction for snap_scaffold_15-snap.1213-T1
Valid prediction for snap_scaffold_15-snap.1237-T1
Valid prediction for GlimmerHMM_glimmerT_36219-T1
Valid prediction for GlimmerHMM_glimmerT_36213-T1
Valid prediction for snap_scaffold_15-snap.1239-T1
Valid prediction for snap_scaffold_15-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_36229-T1
Valid prediction for snap_scaffold_15-snap.1243-T1
Valid prediction for Augustus_model.g24138.t1
Valid prediction for snap_scaffold_15-snap.1218-T1
Couldn't classify 114713, 114731
Sorry, prediction pasa_asmbl_14224.p1 fails validation.
(ATG)	 CA	110340-110535	GT	CAG
(GTC)	 AG	110910-111022	GT	CAG
(TAC)	 AG	111276-111356	GT	AGG
(TTC)	 AG	111600-111729	GT	AGG
(GAA)	 AG	111840-111889	GT	AGG
(GGC)	 AG	112012-112142	GT	AGG
(GGG)	 AG	112426-112543	GT	CTG
(GTC)	 AG	113256-113375	GT	CGG
(TTC)	 AG	113649-113705	GT	AGG
(ATA)	 AG	113988-114099	GT	AGG
(AGC)	 AG	114206-114287	GT	GGG
(AGG)	 AG	114713-114731	GG	CAG
-recovered pasa_asmbl_14224.p1, initial, 110340, 110535
-recovered pasa_asmbl_14224.p1, internal, 110910, 111022
-recovered pasa_asmbl_14224.p1, internal, 111276, 111356
-recovered pasa_asmbl_14224.p1, internal, 111600, 111729
-recovered pasa_asmbl_14224.p1, internal, 111840, 111889
-recovered pasa_asmbl_14224.p1, internal, 112012, 112142
-recovered pasa_asmbl_14224.p1, internal, 112426, 112543
-recovered pasa_asmbl_14224.p1, internal, 113256, 113375
-recovered pasa_asmbl_14224.p1, internal, 113649, 113705
-recovered pasa_asmbl_14224.p1, internal, 113988, 114099
-recovered pasa_asmbl_14224.p1, internal, 114206, 114287
Valid prediction for snap_scaffold_15-snap.1238-T1
Valid prediction for GlimmerHMM_glimmerT_36217-T1
Couldn't classify 102173, 102239
Couldn't classify 105851, 105991
Sorry, prediction pasa_asmbl_14227.p1 fails validation.
(TCA)	 TC	102173-102239	GT	AGG
(TAG)	 AG	102483-102580	GT	AGG
(ATT)	 AG	103903-103933	GT	CTG
(ACC)	 AG	104548-104634	GT	GGG
(AAA)	 AG	104902-105013	GT	AGG
(GAC)	 AG	105694-105715	GT	TGG
(AGT)	 AG	105851-105991	GG	AAG
-recovered pasa_asmbl_14227.p1, internal, 102483, 102580
-recovered pasa_asmbl_14227.p1, internal, 103903, 103933
-recovered pasa_asmbl_14227.p1, internal, 104548, 104634
-recovered pasa_asmbl_14227.p1, internal, 104902, 105013
-recovered pasa_asmbl_14227.p1, internal, 105694, 105715
Valid prediction for Augustus_model.g24134.t1
Valid prediction for snap_scaffold_15-snap.1241-T1
Valid prediction for Augustus_model.g24141.t1
Valid prediction for snap_scaffold_15-snap.1212-T1
Valid prediction for Augustus_model.g24144.t1
Valid prediction for GlimmerHMM_glimmerT_36214-T1
Valid prediction for snap_scaffold_15-snap.1233-T1
Valid prediction for HiQ_model.g24136.t1
Valid prediction for snap_scaffold_15-snap.1240-T1
Valid prediction for snap_scaffold_15-snap.1232-T1
Valid prediction for Augustus_model.g24137.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23872, rend_intergenic: 18395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29704, rend_intergenic: 25515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48280, rend_intergenic: 45525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50411, rend_intergenic: 49005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56385, rend_intergenic: 53184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67472, rend_intergenic: 65133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78055, rend_intergenic: 73222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92803, rend_intergenic: 88604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93843, rend_intergenic: 92843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98335, rend_intergenic: 96125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102445, rend_intergenic: 98611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130552, rend_intergenic: 104050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141805, rend_intergenic: 137194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150069, rend_intergenic: 143049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151982
-exon list size: 384


building trellis

0.3    
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1.0    
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1.6    
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2.1    
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3.9    
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6.2    
6.5    
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7.3    
7.5    
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9.1    
9.3    
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9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
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65.0    
65.3    
65.5    
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66.1    
66.3    
66.6    
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68.1    
68.4    
68.7    
68.9    
69.2    
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69.7    
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72.0    
72.3    
72.5    
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73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
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76.4    
76.7    
76.9    
77.2    
77.5    
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78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 23872, rend_intergenic: 18395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29704, rend_intergenic: 25515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48280, rend_intergenic: 45525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50411, rend_intergenic: 49005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56385, rend_intergenic: 53184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67472, rend_intergenic: 65133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78055, rend_intergenic: 73222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92803, rend_intergenic: 88604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93843, rend_intergenic: 92843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98335, rend_intergenic: 96125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102445, rend_intergenic: 98611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130552, rend_intergenic: 104050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141805, rend_intergenic: 137194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150069, rend_intergenic: 143049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support