-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_17334413-17540787

-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_4-snap.3568-T1
Valid prediction for snap_scaffold_4-snap.3569-T1
Valid prediction for CodingQuarry_transcript_49328-T1
Valid prediction for snap_scaffold_4-snap.3590-T1
Valid prediction for snap_scaffold_4-snap.3551-T1
Valid prediction for CodingQuarry_transcript_49333-T1
Valid prediction for snap_scaffold_4-snap.3576-T1
Valid prediction for snap_scaffold_4-snap.3588-T1
Valid prediction for snap_scaffold_4-snap.3554-T1
Valid prediction for snap_scaffold_4-snap.3560-T1
Valid prediction for snap_scaffold_4-snap.3552-T1
Valid prediction for GlimmerHMM_glimmerT_10997-T1
Valid prediction for HiQ_model.g7224.t1
Valid prediction for GlimmerHMM_glimmerT_11014-T1
Valid prediction for GlimmerHMM_glimmerT_10988-T1
Valid prediction for snap_scaffold_4-snap.3582-T1
Valid prediction for snap_scaffold_4-snap.3556-T1
Valid prediction for GlimmerHMM_glimmerT_10993-T1
Valid prediction for snap_scaffold_4-snap.3580-T1
Valid prediction for GlimmerHMM_glimmerT_10994-T1
Valid prediction for GlimmerHMM_glimmerT_11015-T1
Valid prediction for GlimmerHMM_glimmerT_11007-T1
Valid prediction for snap_scaffold_4-snap.3574-T1
Valid prediction for GlimmerHMM_glimmerT_11010-T1
Valid prediction for snap_scaffold_4-snap.3563-T1
Valid prediction for snap_scaffold_4-snap.3550-T1
Valid prediction for snap_scaffold_4-snap.3587-T1
Valid prediction for GlimmerHMM_glimmerT_10987-T1
Valid prediction for snap_scaffold_4-snap.3571-T1
Valid prediction for Augustus_model.g7212.t1
Valid prediction for GlimmerHMM_glimmerT_11002-T1
Valid prediction for snap_scaffold_4-snap.3585-T1
Valid prediction for snap_scaffold_4-snap.3593-T1
Valid prediction for HiQ_model.g7220.t1
Valid prediction for Augustus_model.g7223.t1
Valid prediction for snap_scaffold_4-snap.3584-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10998-T1
Valid prediction for pasa_asmbl_42051.p1
Valid prediction for snap_scaffold_4-snap.3555-T1
Valid prediction for snap_scaffold_4-snap.3566-T1
Valid prediction for snap_scaffold_4-snap.3565-T1
Valid prediction for snap_scaffold_4-snap.3591-T1
Valid prediction for GlimmerHMM_glimmerT_10989-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_11012-T1
Valid prediction for snap_scaffold_4-snap.3557-T1
Valid prediction for snap_scaffold_4-snap.3572-T1
Valid prediction for snap_scaffold_4-snap.3558-T1
Valid prediction for GlimmerHMM_glimmerT_10995-T1
Valid prediction for pasa_asmbl_43278.p1
Valid prediction for GlimmerHMM_glimmerT_11000-T1
Valid prediction for HiQ_model.g7219.t1
Valid prediction for Augustus_model.g7211.t1
Valid prediction for GlimmerHMM_glimmerT_10996-T1
Couldn't classify 46885, 47217
Sorry, prediction pasa_asmbl_43277.p1 fails validation.
(ATG)	 AC	45233-45235	GT	TGG
(AAC)	 AG	45904-46051	GT	AGG
(AGG)	 AG	46331-46521	GT	TTG
(ACC)	 AG	46885-47217	AA	ATA
-recovered pasa_asmbl_43277.p1, initial, 45233, 45235
-recovered pasa_asmbl_43277.p1, internal, 45904, 46051
-recovered pasa_asmbl_43277.p1, internal, 46331, 46521
Valid prediction for Augustus_model.g7213.t1
Valid prediction for snap_scaffold_4-snap.3573-T1
Valid prediction for CodingQuarry_transcript_49332-T1
Valid prediction for snap_scaffold_4-snap.3559-T1
Valid prediction for snap_scaffold_4-snap.3561-T1
Valid prediction for snap_scaffold_4-snap.3594-T1
Valid prediction for snap_scaffold_4-snap.3577-T1
Couldn't classify 67365, 68117
Sorry, prediction pasa_asmbl_43270.p1 fails validation.
(TTC)	 GG	67365-68117	AG	CCA
Couldn't classify 116858, 117385
Sorry, prediction pasa_asmbl_43621.p1 fails validation.
(ACC)	 GT	116858-117385	GT	AGG
(TCG)	 AG	117563-117658	GT	AGG
(GTC)	 AG	117862-117999	GT	AGG
(ATG)	 AG	118578-118665	GT	GGG
(AGT)	 AG	118815-119245	AG	GAA
-recovered pasa_asmbl_43621.p1, initial, 118578, 118665
-recovered pasa_asmbl_43621.p1, terminal, 118815, 119245
-recovered pasa_asmbl_43621.p1, internal, 117563, 117658
-recovered pasa_asmbl_43621.p1, internal, 117862, 117999
-recovered pasa_asmbl_43621.p1, internal, 118578, 118665
Valid prediction for snap_scaffold_4-snap.3586-T1
Valid prediction for GlimmerHMM_glimmerT_10992-T1
Valid prediction for Augustus_model.g7217.t1
Couldn't classify 116280, 116421
Sorry, prediction pasa_asmbl_43264.p1 fails validation.
(ATG)	 TC	107626-107680	GT	AGG
(TCT)	 AG	110157-110210	GT	TGG
(GGT)	 AG	110636-110691	GT	TGG
(CGT)	 AG	111181-111247	GT	AGG
(TCA)	 AG	113018-113143	GT	CCG
(ACC)	 AG	113434-113630	GT	AGG
(CCT)	 AG	113799-113939	GT	AGG
(ACA)	 AG	114819-114984	GT	AGG
(GGG)	 AG	115362-115557	GT	AGG
(CGG)	 AG	116280-116421	AG	TGA
-recovered pasa_asmbl_43264.p1, initial, 107626, 107680
-recovered pasa_asmbl_43264.p1, internal, 110157, 110210
-recovered pasa_asmbl_43264.p1, internal, 110636, 110691
-recovered pasa_asmbl_43264.p1, internal, 111181, 111247
-recovered pasa_asmbl_43264.p1, internal, 113018, 113143
-recovered pasa_asmbl_43264.p1, internal, 113434, 113630
-recovered pasa_asmbl_43264.p1, internal, 113799, 113939
-recovered pasa_asmbl_43264.p1, internal, 114819, 114984
-recovered pasa_asmbl_43264.p1, internal, 115362, 115557
Valid prediction for GlimmerHMM_glimmerT_10999-T1
Valid prediction for Augustus_model.g7221.t1
Couldn't classify 91109, 91209
Sorry, prediction pasa_asmbl_43552.p1 fails validation.
(CCC)	 CC	91109-91209	GT	GGG
(ACA)	 AG	91704-91780	GT	GAG
(AGA)	 AG	92347-92529	GT	AGG
(CTC)	 AG	92654-92851	GT	TGG
(AAC)	 AG	93071-93153	TG	GAT
-recovered pasa_asmbl_43552.p1, terminal, 93071, 93153
-recovered pasa_asmbl_43552.p1, internal, 91704, 91780
-recovered pasa_asmbl_43552.p1, internal, 92347, 92529
-recovered pasa_asmbl_43552.p1, internal, 92654, 92851
Valid prediction for GlimmerHMM_glimmerT_11004-T1
Valid prediction for GlimmerHMM_glimmerT_11013-T1
Valid prediction for CodingQuarry_transcript_49331-T1
Valid prediction for GlimmerHMM_glimmerT_10991-T1
Valid prediction for pasa_asmbl_43267.p1
Valid prediction for snap_scaffold_4-snap.3578-T1
Valid prediction for Augustus_model.g7218.t1
Valid prediction for pasa_asmbl_43281.p1
Valid prediction for GlimmerHMM_glimmerT_11008-T1
Valid prediction for snap_scaffold_4-snap.3570-T1
Valid prediction for snap_scaffold_4-snap.3567-T1
Valid prediction for snap_scaffold_4-snap.3553-T1
Valid prediction for GlimmerHMM_glimmerT_11003-T1
Valid prediction for GlimmerHMM_glimmerT_10990-T1
Valid prediction for CodingQuarry_transcript_49327-T1
Valid prediction for snap_scaffold_4-snap.3575-T1
Valid prediction for GlimmerHMM_glimmerT_11011-T1
Valid prediction for CodingQuarry_transcript_49329-T1
Valid prediction for snap_scaffold_4-snap.3581-T1
Valid prediction for GlimmerHMM_glimmerT_11009-T1
Valid prediction for snap_scaffold_4-snap.3583-T1
Valid prediction for Augustus_model.g7215.t1
Couldn't classify 86028, 86178
Couldn't classify 86814, 86989
Sorry, prediction pasa_asmbl_43623.p1 fails validation.
(CCA)	 CT	86028-86178	GT	AGG
(GTC)	 AG	86814-86989	GA	ATG
Valid prediction for snap_scaffold_4-snap.3592-T1
Valid prediction for CodingQuarry_transcript_49330-T1
Valid prediction for snap_scaffold_4-snap.3579-T1
Valid prediction for Augustus_model.g7216.t1
Valid prediction for snap_scaffold_4-snap.3589-T1
Valid prediction for Augustus_model.g7222.t1
Valid prediction for GlimmerHMM_glimmerT_11001-T1
Valid prediction for GlimmerHMM_glimmerT_11005-T1
Valid prediction for GlimmerHMM_glimmerT_11006-T1
Valid prediction for snap_scaffold_4-snap.3564-T1
Valid prediction for snap_scaffold_4-snap.3562-T1
Valid prediction for Augustus_model.g7214.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25216, rend_intergenic: 22057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48090, rend_intergenic: 25635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62902, rend_intergenic: 48255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69954, rend_intergenic: 63699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79679, rend_intergenic: 72376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87596, rend_intergenic: 84106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95201, rend_intergenic: 87603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103671, rend_intergenic: 98411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104467, rend_intergenic: 103817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118118, rend_intergenic: 112886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123063, rend_intergenic: 119424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183197, rend_intergenic: 171091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193107, rend_intergenic: 186356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197299, rend_intergenic: 196168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200594, rend_intergenic: 198995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201883, rend_intergenic: 201316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203452, rend_intergenic: 202030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206375
-exon list size: 361


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 25216, rend_intergenic: 22057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48090, rend_intergenic: 25635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62902, rend_intergenic: 48255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69954, rend_intergenic: 63699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79679, rend_intergenic: 72376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87596, rend_intergenic: 84106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95201, rend_intergenic: 87603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103671, rend_intergenic: 98411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104467, rend_intergenic: 103817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118118, rend_intergenic: 112886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123063, rend_intergenic: 119424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183197, rend_intergenic: 171091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193107, rend_intergenic: 186356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197299, rend_intergenic: 196168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200594, rend_intergenic: 198995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201883, rend_intergenic: 201316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203452, rend_intergenic: 202030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support
	-no exons in range 1 - 13046