-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15019321-15180482

-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_10667-T1
Valid prediction for GlimmerHMM_glimmerT_10657-T1
Valid prediction for snap_scaffold_4-snap.3024-T1
Valid prediction for snap_scaffold_4-snap.3031-T1
Valid prediction for snap_scaffold_4-snap.3016-T1
Valid prediction for snap_scaffold_4-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_10666-T1
Valid prediction for Augustus_model.g6998.t1
Valid prediction for Augustus_model.g7000.t1
Valid prediction for snap_scaffold_4-snap.3020-T1
Valid prediction for Augustus_model.g7010.t1
Valid prediction for snap_scaffold_4-snap.3006-T1
Valid prediction for GlimmerHMM_glimmerT_10656-T1
Valid prediction for snap_scaffold_4-snap.3030-T1
Valid prediction for Augustus_model.g6997.t1
Valid prediction for GlimmerHMM_glimmerT_10659-T1
Valid prediction for GlimmerHMM_glimmerT_10653-T1
Valid prediction for Augustus_model.g6991.t1
Valid prediction for Augustus_model.g7011.t1
Valid prediction for GlimmerHMM_glimmerT_10672-T1
Valid prediction for Augustus_model.g7004.t1
Valid prediction for snap_scaffold_4-snap.2994-T1
Valid prediction for snap_scaffold_4-snap.3018-T1
Valid prediction for snap_scaffold_4-snap.3028-T1
Valid prediction for snap_scaffold_4-snap.3027-T1
Valid prediction for GlimmerHMM_glimmerT_10645-T1
Valid prediction for snap_scaffold_4-snap.3032-T1
Valid prediction for snap_scaffold_4-snap.3003-T1
Valid prediction for Augustus_model.g6995.t1
Valid prediction for snap_scaffold_4-snap.3034-T1
Valid prediction for Augustus_model.g7003.t1
Valid prediction for GlimmerHMM_glimmerT_10651-T1
Valid prediction for snap_scaffold_4-snap.3013-T1
Valid prediction for GlimmerHMM_glimmerT_10654-T1
Valid prediction for GlimmerHMM_glimmerT_10643-T1
Valid prediction for GlimmerHMM_glimmerT_10668-T1
Valid prediction for HiQ_model.g6993.t1
Couldn't classify 140008, 140092
Couldn't classify 145362, 145504
Sorry, prediction pasa_asmbl_41930.p1 fails validation.
(GCT)	 CA	140008-140092	GT	AAG
(GAC)	 AG	140895-141074	GT	CGG
(GGG)	 AG	141220-141390	GT	GGG
(TGG)	 AG	141635-141735	GT	AGG
(CTT)	 AG	141851-141967	GT	AGG
(CCG)	 AG	142228-142311	GT	TGG
(ATC)	 AG	142476-142556	GT	AGG
(GTC)	 AG	142891-143042	GT	AGG
(ATC)	 AG	143278-143410	GT	AGG
(TAC)	 AG	143654-143742	GT	GAG
(CGG)	 AG	143900-143994	GT	GGG
(GGG)	 AG	144382-144444	GT	GGG
(ATG)	 AG	144623-144666	GT	TGG
(GTT)	 AG	144763-144859	GT	GAG
(GAA)	 AG	144981-145036	GT	AGG
(GTG)	 AG	145150-145246	GT	GGG
(ATC)	 AG	145362-145504	AG	CAA
-recovered pasa_asmbl_41930.p1, initial, 144623, 144666
add_exon() Sorry, pasa_asmbl_41930.p1 143654-143742-terminal-2 is invalid.
-recovered pasa_asmbl_41930.p1, terminal, 143654, 143742
add_exon() Sorry, pasa_asmbl_41930.p1 144763-144859-terminal-3 is invalid.
-recovered pasa_asmbl_41930.p1, terminal, 144763, 144859
-recovered pasa_asmbl_41930.p1, internal, 140895, 141074
-recovered pasa_asmbl_41930.p1, internal, 141220, 141390
-recovered pasa_asmbl_41930.p1, internal, 141635, 141735
-recovered pasa_asmbl_41930.p1, internal, 141851, 141967
-recovered pasa_asmbl_41930.p1, internal, 142228, 142311
-recovered pasa_asmbl_41930.p1, internal, 142476, 142556
-recovered pasa_asmbl_41930.p1, internal, 142891, 143042
-recovered pasa_asmbl_41930.p1, internal, 143278, 143410
-recovered pasa_asmbl_41930.p1, internal, 143654, 143742
-recovered pasa_asmbl_41930.p1, internal, 143900, 143994
-recovered pasa_asmbl_41930.p1, internal, 144382, 144444
-recovered pasa_asmbl_41930.p1, internal, 144623, 144666
-recovered pasa_asmbl_41930.p1, internal, 144763, 144859
-recovered pasa_asmbl_41930.p1, internal, 144981, 145036
-recovered pasa_asmbl_41930.p1, internal, 145150, 145246
Valid prediction for snap_scaffold_4-snap.3015-T1
Valid prediction for GlimmerHMM_glimmerT_10647-T1
Valid prediction for GlimmerHMM_glimmerT_10658-T1
Valid prediction for snap_scaffold_4-snap.3022-T1
Valid prediction for snap_scaffold_4-snap.3007-T1
Couldn't classify 91024, 91198
Sorry, prediction pasa_asmbl_41928.p1 fails validation.
(AGG)	 GA	91024-91198	GT	GGG
(GTT)	 AG	91481-91569	GT	AGG
(GAG)	 AG	91927-92170	GT	AGG
(TAG)	 AG	94904-95139	GT	GGG
(CTG)	 AG	95383-95544	GT	AGG
(AGA)	 AG	95685-95811	GT	TGG
(TGT)	 AG	95889-96089	GT	AGG
(CCT)	 AG	96431-96595	GT	AGG
(AAA)	 AG	96717-96842	GT	AGG
(GAG)	 AG	97156-97290	GT	AGG
(GTT)	 AG	97595-97728	GT	ACG
(GAG)	 AG	97986-98105	TG	GAT
-recovered pasa_asmbl_41928.p1, terminal, 97986, 98105
-recovered pasa_asmbl_41928.p1, internal, 91481, 91569
-recovered pasa_asmbl_41928.p1, internal, 91927, 92170
-recovered pasa_asmbl_41928.p1, internal, 94904, 95139
-recovered pasa_asmbl_41928.p1, internal, 95383, 95544
-recovered pasa_asmbl_41928.p1, internal, 95685, 95811
-recovered pasa_asmbl_41928.p1, internal, 95889, 96089
-recovered pasa_asmbl_41928.p1, internal, 96431, 96595
-recovered pasa_asmbl_41928.p1, internal, 96717, 96842
-recovered pasa_asmbl_41928.p1, internal, 97156, 97290
-recovered pasa_asmbl_41928.p1, internal, 97595, 97728
Valid prediction for snap_scaffold_4-snap.3019-T1
Valid prediction for CodingQuarry_transcript_49248-T1
Valid prediction for Augustus_model.g6999.t1
Valid prediction for GlimmerHMM_glimmerT_10661-T1
Valid prediction for snap_scaffold_4-snap.2998-T1
Valid prediction for snap_scaffold_4-snap.3005-T1
Valid prediction for Augustus_model.g6996.t1
Valid prediction for GlimmerHMM_glimmerT_10671-T1
Valid prediction for Augustus_model.g7002.t1
Valid prediction for Augustus_model.g7007.t1
Valid prediction for snap_scaffold_4-snap.3026-T1
Valid prediction for HiQ_model.g7009.t1
Valid prediction for GlimmerHMM_glimmerT_10664-T1
Couldn't classify 13519, 13929
Sorry, prediction pasa_asmbl_41925.p2 fails validation.
(CGC)	 CC	13519-13929	GA	AAG
Valid prediction for snap_scaffold_4-snap.3035-T1
Valid prediction for GlimmerHMM_glimmerT_10665-T1
Valid prediction for HiQ_model.g7005.t1
Couldn't classify 145362, 145504
Sorry, prediction pasa_asmbl_41931.p1 fails validation.
(ATG)	 AC	144772-144859	GT	GAG
(GAA)	 AG	144981-145036	GT	AGG
(GTG)	 AG	145150-145246	GT	GGG
(ATC)	 AG	145362-145504	AG	CAA
-recovered pasa_asmbl_41931.p1, initial, 144772, 144859
-recovered pasa_asmbl_41931.p1, internal, 144981, 145036
-recovered pasa_asmbl_41931.p1, internal, 145150, 145246
Valid prediction for snap_scaffold_4-snap.3011-T1
Valid prediction for snap_scaffold_4-snap.3001-T1
Couldn't classify 148608, 148816
Couldn't classify 149259, 149466
Sorry, prediction pasa_asmbl_42220.p2 fails validation.
(TCT)	 AG	148608-148816	GT	AGG
(GTC)	 AG	149259-149466	GA	CAG
-recovered pasa_asmbl_42220.p2, internal, 148608, 148816

-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_10648-T1
Couldn't classify 151551, 151606
Sorry, prediction pasa_asmbl_43085.p1 fails validation.
(CTG)	 CA	151551-151606	GT	GGG
(TGG)	 AG	151746-151900	GT	AGG
(AGG)	 AG	152138-152244	GT	GAG
(GAT)	 AG	152859-153049	GT	TGG
(GGA)	 AG	153375-153508	GT	AGG
(GTT)	 AG	153983-154047	GT	ATG
(GTT)	 AG	154232-154314	GT	CGG
(GAA)	 AG	154841-155018	GA	GAG
-recovered pasa_asmbl_43085.p1, terminal, 154841, 155018
-recovered pasa_asmbl_43085.p1, internal, 151746, 151900
-recovered pasa_asmbl_43085.p1, internal, 152138, 152244
-recovered pasa_asmbl_43085.p1, internal, 152859, 153049
-recovered pasa_asmbl_43085.p1, internal, 153375, 153508
-recovered pasa_asmbl_43085.p1, internal, 153983, 154047
-recovered pasa_asmbl_43085.p1, internal, 154232, 154314
Valid prediction for pasa_asmbl_43089.p2
Valid prediction for GlimmerHMM_glimmerT_10663-T1
Valid prediction for snap_scaffold_4-snap.2996-T1
Valid prediction for GlimmerHMM_glimmerT_10652-T1
Valid prediction for GlimmerHMM_glimmerT_10644-T1
Valid prediction for Augustus_model.g7001.t1
Valid prediction for snap_scaffold_4-snap.3000-T1
Valid prediction for HiQ_model.g6992.t1
Valid prediction for snap_scaffold_4-snap.3010-T1
Valid prediction for snap_scaffold_4-snap.3025-T1
Valid prediction for snap_scaffold_4-snap.3012-T1
Valid prediction for GlimmerHMM_glimmerT_10670-T1
Valid prediction for Augustus_model.g7008.t1
Valid prediction for CodingQuarry_transcript_49250-T1
Valid prediction for snap_scaffold_4-snap.2995-T1
Valid prediction for snap_scaffold_4-snap.3002-T1
Valid prediction for GlimmerHMM_glimmerT_10662-T1
Valid prediction for snap_scaffold_4-snap.3017-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3029-T1
Valid prediction for snap_scaffold_4-snap.2999-T1
Valid prediction for GlimmerHMM_glimmerT_10660-T1
Valid prediction for snap_scaffold_4-snap.3033-T1
Valid prediction for snap_scaffold_4-snap.3021-T1
Valid prediction for GlimmerHMM_glimmerT_10646-T1
Valid prediction for snap_scaffold_4-snap.3008-T1
Valid prediction for snap_scaffold_4-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_10669-T1
Valid prediction for Augustus_model.g6994.t1
Valid prediction for GlimmerHMM_glimmerT_10649-T1
Valid prediction for GlimmerHMM_glimmerT_10650-T1
Valid prediction for snap_scaffold_4-snap.3004-T1
Valid prediction for Augustus_model.g7006.t1
Valid prediction for GlimmerHMM_glimmerT_10655-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3014-T1
Valid prediction for HiQ_model.g7012.t1
Valid prediction for GlimmerHMM_glimmerT_10673-T1
Valid prediction for snap_scaffold_4-snap.3009-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24922, rend_intergenic: 23681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25984, rend_intergenic: 25294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30644, rend_intergenic: 27312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31117, rend_intergenic: 31024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38034, rend_intergenic: 31508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48263, rend_intergenic: 38059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68435, rend_intergenic: 54395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69579, rend_intergenic: 68976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74491, rend_intergenic: 71110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80999, rend_intergenic: 75979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85357, rend_intergenic: 81320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118043, rend_intergenic: 114216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136255, rend_intergenic: 126957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161162
-exon list size: 370


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 24922, rend_intergenic: 23681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25984, rend_intergenic: 25294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30644, rend_intergenic: 27312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31117, rend_intergenic: 31024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38034, rend_intergenic: 31508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48263, rend_intergenic: 38059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68435, rend_intergenic: 54395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69579, rend_intergenic: 68976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74491, rend_intergenic: 71110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80999, rend_intergenic: 75979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85357, rend_intergenic: 81320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118043, rend_intergenic: 114216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136255, rend_intergenic: 126957  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