-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_7711371-7920040

-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: +)Couldn't classify 178911, 179027
Sorry, prediction pasa_asmbl_45519.p1 fails validation.
(GCA)	 AG	178911-179027	GT	AGG
(GGC)	 AG	179478-179593	GT	AGG
(TTT)	 AG	180026-180324	GT	ATG
(TCA)	 AG	180443-180756	GT	AGG
(GAG)	 AG	181847-182077	GT	AGG
(ATC)	 AG	182979-183173	AC	AAA
-recovered pasa_asmbl_45519.p1, terminal, 182979, 183173
-recovered pasa_asmbl_45519.p1, internal, 178911, 179027
-recovered pasa_asmbl_45519.p1, internal, 179478, 179593
-recovered pasa_asmbl_45519.p1, internal, 180026, 180324
-recovered pasa_asmbl_45519.p1, internal, 180443, 180756
-recovered pasa_asmbl_45519.p1, internal, 181847, 182077
Valid prediction for GlimmerHMM_glimmerT_12230-T1
Valid prediction for GlimmerHMM_glimmerT_12227-T1
Couldn't classify 102694, 102756
Couldn't classify 109652, 109787
Sorry, prediction pasa_asmbl_45515.p1 fails validation.
(TGC)	 AC	102694-102756	GT	TGG
(GAT)	 AG	103655-103745	GT	AAG
(TAC)	 AG	104518-104570	GT	AGG
(GAC)	 AG	104771-104959	GT	AGG
(GAT)	 AG	107575-107672	GT	CGG
(GTT)	 AG	108242-108328	GT	CGG
(ATT)	 AG	109652-109787	GT	AGG
-recovered pasa_asmbl_45515.p1, internal, 103655, 103745
-recovered pasa_asmbl_45515.p1, internal, 104518, 104570
-recovered pasa_asmbl_45515.p1, internal, 104771, 104959
-recovered pasa_asmbl_45515.p1, internal, 107575, 107672
-recovered pasa_asmbl_45515.p1, internal, 108242, 108328
-recovered pasa_asmbl_45515.p1, internal, 109652, 109787
Valid prediction for snap_scaffold_5-snap.1512-T1
Valid prediction for Augustus_model.g8039.t1
Valid prediction for snap_scaffold_5-snap.1499-T1
Valid prediction for Augustus_model.g8042.t1
Valid prediction for snap_scaffold_5-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_12228-T1
Valid prediction for GlimmerHMM_glimmerT_12223-T1
Valid prediction for snap_scaffold_5-snap.1516-T1
Valid prediction for GlimmerHMM_glimmerT_12235-T1
Couldn't classify 110051, 110093
Couldn't classify 113046, 113135
Sorry, prediction pasa_asmbl_46332.p1 fails validation.
(CCT)	 CC	110051-110093	GT	TGG
(GCT)	 AG	110468-110587	GT	AGG
(TTA)	 AG	112378-112457	GT	AGG
(GAC)	 AG	113046-113135	GT	AGG
-recovered pasa_asmbl_46332.p1, internal, 110468, 110587
-recovered pasa_asmbl_46332.p1, internal, 112378, 112457
-recovered pasa_asmbl_46332.p1, internal, 113046, 113135
Valid prediction for GlimmerHMM_glimmerT_12231-T1
Valid prediction for Augustus_model.g8038.t1
Valid prediction for GlimmerHMM_glimmerT_12225-T1
Valid prediction for GlimmerHMM_glimmerT_12219-T1
Valid prediction for snap_scaffold_5-snap.1521-T1
Valid prediction for snap_scaffold_5-snap.1520-T1
Valid prediction for Augustus_model.g8041.t1
Valid prediction for Augustus_model.g8034.t1
Valid prediction for GlimmerHMM_glimmerT_12215-T1
Couldn't classify 129385, 130275
Sorry, prediction pasa_asmbl_45518.p1 fails validation.
(ATG)	 AC	129385-130275	AG	AGA
Valid prediction for CodingQuarry_transcript_52130-T1
Valid prediction for GlimmerHMM_glimmerT_12220-T1
Valid prediction for Augustus_model.g8043.t1
Valid prediction for GlimmerHMM_glimmerT_12233-T1
Valid prediction for GlimmerHMM_glimmerT_12224-T1
Valid prediction for HiQ_model.g8035.t1
Valid prediction for snap_scaffold_5-snap.1495-T1
Valid prediction for CodingQuarry_transcript_52129-T1
Couldn't classify 20741, 21325
Sorry, prediction pasa_asmbl_45504.p1 fails validation.
(GTC)	 GG	20741-21325	GT	AGG
(GTT)	 AG	21503-21964	GT	AGG
(ACC)	 AG	22060-22176	GT	AGG
(ATT)	 AG	22526-22641	GT	AAG
(ATA)	 AG	23365-23467	GT	AGG
(ATC)	 AG	23891-23980	GT	TGG
(AAA)	 AG	24897-25118	TG	AGT
-recovered pasa_asmbl_45504.p1, terminal, 24897, 25118
-recovered pasa_asmbl_45504.p1, internal, 21503, 21964
-recovered pasa_asmbl_45504.p1, internal, 22060, 22176
-recovered pasa_asmbl_45504.p1, internal, 22526, 22641
-recovered pasa_asmbl_45504.p1, internal, 23365, 23467
-recovered pasa_asmbl_45504.p1, internal, 23891, 23980
Valid prediction for snap_scaffold_5-snap.1505-T1
Valid prediction for pasa_asmbl_45507.p1
Valid prediction for GlimmerHMM_glimmerT_12221-T1
Valid prediction for GlimmerHMM_glimmerT_12222-T1
Valid prediction for Augustus_model.g8037.t1
Valid prediction for snap_scaffold_5-snap.1504-T1
Valid prediction for snap_scaffold_5-snap.1507-T1
Valid prediction for snap_scaffold_5-snap.1503-T1
Valid prediction for snap_scaffold_5-snap.1509-T1
Valid prediction for snap_scaffold_5-snap.1510-T1
Valid prediction for snap_scaffold_5-snap.1517-T1
Valid prediction for GlimmerHMM_glimmerT_12216-T1
Valid prediction for snap_scaffold_5-snap.1515-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_12226-T1
Valid prediction for GlimmerHMM_glimmerT_12236-T1
Valid prediction for GlimmerHMM_glimmerT_12229-T1
Valid prediction for snap_scaffold_5-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_12214-T1
Valid prediction for snap_scaffold_5-snap.1498-T1
Valid prediction for snap_scaffold_5-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_12232-T1
Valid prediction for Augustus_model.g8040.t1
Valid prediction for snap_scaffold_5-snap.1513-T1
Couldn't classify 202592, 202660
Sorry, prediction CodingQuarry_transcript_52128-T1 fails validation.
(ATG)	 CG	201839-201868	GT	AGG
(GTG)	 AG	202060-202198	GT	CCG
(CTC)	 AG	202592-202660	TG	GGT
(CAT)	 AG	203926-204012	GT	AGG
(GGA)	 AG	204488-204633	AT	GAA
-recovered CodingQuarry_transcript_52128-T1, initial, 201839, 201868
-recovered CodingQuarry_transcript_52128-T1, terminal, 204488, 204633
-recovered CodingQuarry_transcript_52128-T1, internal, 202060, 202198
-recovered CodingQuarry_transcript_52128-T1, internal, 203926, 204012
Valid prediction for Augustus_model.g8036.t1
Valid prediction for snap_scaffold_5-snap.1500-T1
Valid prediction for snap_scaffold_5-snap.1514-T1
Valid prediction for snap_scaffold_5-snap.1494-T1
Valid prediction for snap_scaffold_5-snap.1501-T1
Valid prediction for snap_scaffold_5-snap.1492-T1
Valid prediction for snap_scaffold_5-snap.1502-T1
Valid prediction for snap_scaffold_5-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_12234-T1
Valid prediction for GlimmerHMM_glimmerT_12217-T1
Valid prediction for snap_scaffold_5-snap.1493-T1
Valid prediction for Augustus_model.g8033.t1
Valid prediction for snap_scaffold_5-snap.1518-T1
Valid prediction for snap_scaffold_5-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_12218-T1
Couldn't classify 197465, 197557
Couldn't classify 201109, 201147
Sorry, prediction pasa_asmbl_44985.p1 fails validation.
(CGC)	 GA	197465-197557	GT	AGG
(TTC)	 AG	199653-199853	GC	AGG
(ATG)	 AG	200679-200774	GT	GTG
(GAA)	 AG	201109-201147	GC	AAG
-recovered pasa_asmbl_44985.p1, initial, 200679, 200774
-recovered pasa_asmbl_44985.p1, internal, 199653, 199853
-recovered pasa_asmbl_44985.p1, internal, 200679, 200774
-recovered pasa_asmbl_44985.p1, internal, 201109, 201147
Valid prediction for snap_scaffold_5-snap.1519-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 82122, rend_intergenic: 76813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95451, rend_intergenic: 94538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113221, rend_intergenic: 109979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151772, rend_intergenic: 145191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164101, rend_intergenic: 156340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183173, rend_intergenic: 179468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208670
-exon list size: 251


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.2    
18.6    
19.0    
19.4    
19.8    
20.2    
20.6    
20.9    
21.3    
21.7    
22.1    
22.5    
22.9    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.9    
27.3    
27.7    
28.1    
28.5    
28.9    
29.2    
29.6    
30.0    
30.4    
30.8    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.9    
40.3    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.7    
60.1    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.2    
69.6    
70.0    
70.4    
70.8    
71.1    
71.5    
71.9    
72.3    
72.7    
73.1    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.1    
77.5    
77.9    
78.3    
78.7    
79.1    
79.4    
79.8    
80.2    
80.6    
81.0    
81.4    
81.8    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 82122, rend_intergenic: 76813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95451, rend_intergenic: 94538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113221, rend_intergenic: 109979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151772, rend_intergenic: 145191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164101, rend_intergenic: 156340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183173, rend_intergenic: 179468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support