-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_13132914-13528576

-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_10472-T1
Valid prediction for Augustus_model.g6836.t1
Valid prediction for GlimmerHMM_glimmerT_10473-T1
Valid prediction for snap_scaffold_4-snap.2756-T1
Valid prediction for snap_scaffold_4-snap.2783-T1
Valid prediction for Augustus_model.g6853.t1
Valid prediction for snap_scaffold_4-snap.2785-T1
Valid prediction for GlimmerHMM_glimmerT_10486-T1
Valid prediction for snap_scaffold_4-snap.2762-T1
Valid prediction for HiQ_model.g6850.t1
Valid prediction for GlimmerHMM_glimmerT_10475-T1
Valid prediction for snap_scaffold_4-snap.2758-T1
Valid prediction for GlimmerHMM_glimmerT_10468-T1
Valid prediction for GlimmerHMM_glimmerT_10466-T1
Valid prediction for GlimmerHMM_glimmerT_10480-T1
Valid prediction for Augustus_model.g6837.t1
Valid prediction for CodingQuarry_transcript_49189-T1
Valid prediction for snap_scaffold_4-snap.2794-T1
Valid prediction for Augustus_model.g6839.t1
Valid prediction for GlimmerHMM_glimmerT_10488-T1
Valid prediction for pasa_asmbl_41795.p1
Valid prediction for CodingQuarry_transcript_49190-T1
Valid prediction for snap_scaffold_4-snap.2767-T1
Valid prediction for GlimmerHMM_glimmerT_10484-T1
Valid prediction for snap_scaffold_4-snap.2790-T1
Valid prediction for pasa_asmbl_41788.p1
Valid prediction for snap_scaffold_4-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_10476-T1
Valid prediction for snap_scaffold_4-snap.2789-T1
Couldn't classify 253528, 253631
Sorry, prediction pasa_asmbl_41785.p1 fails validation.
(GGT)	 AG	253528-253631	GT	AGG
(CGA)	 AG	255969-256044	GT	AGG
(AAA)	 AG	256522-257100	AA	AGA
-recovered pasa_asmbl_41785.p1, terminal, 256522, 257100
-recovered pasa_asmbl_41785.p1, internal, 253528, 253631
-recovered pasa_asmbl_41785.p1, internal, 255969, 256044
Couldn't classify 239917, 239937
Couldn't classify 241699, 242118
Sorry, prediction pasa_asmbl_41784.p1 fails validation.
(ATT)	 TC	239917-239937	GT	AGG
(CAG)	 AG	241699-242118	AA	AGA
Valid prediction for snap_scaffold_4-snap.2792-T1
Valid prediction for snap_scaffold_4-snap.2768-T1
Valid prediction for snap_scaffold_4-snap.2771-T1
Couldn't classify 38582, 38840
Couldn't classify 39418, 39539
Sorry, prediction pasa_asmbl_42164.p1 fails validation.
(TCA)	 CT	38582-38840	GT	CGG
(GTA)	 AG	39418-39539	AA	ACA
Valid prediction for GlimmerHMM_glimmerT_10482-T1
Valid prediction for CodingQuarry_transcript_49191-T1
Valid prediction for GlimmerHMM_glimmerT_10461-T1
Valid prediction for Augustus_model.g6834.t1
Valid prediction for snap_scaffold_4-snap.2796-T1
Valid prediction for snap_scaffold_4-snap.2779-T1
Valid prediction for snap_scaffold_4-snap.2795-T1
Valid prediction for Augustus_model.g6838.t1
Valid prediction for Augustus_model.g6843.t1
Valid prediction for snap_scaffold_4-snap.2786-T1
Valid prediction for snap_scaffold_4-snap.2763-T1
Valid prediction for snap_scaffold_4-snap.2778-T1
Valid prediction for snap_scaffold_4-snap.2791-T1
Valid prediction for HiQ_model.g6848.t1
Valid prediction for GlimmerHMM_glimmerT_10474-T1
Valid prediction for Augustus_model.g6842.t1
Valid prediction for CodingQuarry_transcript_49192-T1
Valid prediction for GlimmerHMM_glimmerT_10459-T1
Valid prediction for GlimmerHMM_glimmerT_10470-T1
Valid prediction for CodingQuarry_transcript_49188-T1
Valid prediction for snap_scaffold_4-snap.2777-T1
Valid prediction for Augustus_model.g6832.t1
Valid prediction for pasa_asmbl_41794.p1
Valid prediction for CodingQuarry_transcript_49194-T1
Valid prediction for snap_scaffold_4-snap.2764-T1
Valid prediction for CodingQuarry_transcript_49193-T1
Valid prediction for GlimmerHMM_glimmerT_10463-T1
Valid prediction for GlimmerHMM_glimmerT_10467-T1
Valid prediction for snap_scaffold_4-snap.2765-T1
Valid prediction for Augustus_model.g6844.t1
Valid prediction for Augustus_model.g6852.t1
Valid prediction for CodingQuarry_transcript_49186-T1
Valid prediction for snap_scaffold_4-snap.2760-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 Augustus_model.g6841.t1
Valid prediction for GlimmerHMM_glimmerT_10485-T1
Valid prediction for HiQ_model.g6835.t1
Valid prediction for GlimmerHMM_glimmerT_10458-T1
Valid prediction for GlimmerHMM_glimmerT_10462-T1
Valid prediction for GlimmerHMM_glimmerT_10464-T1
Valid prediction for CodingQuarry_transcript_49184-T1
Valid prediction for snap_scaffold_4-snap.2775-T1
Valid prediction for snap_scaffold_4-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_10469-T1
Valid prediction for snap_scaffold_4-snap.2766-T1
Valid prediction for snap_scaffold_4-snap.2780-T1
Valid prediction for GlimmerHMM_glimmerT_10471-T1
Valid prediction for snap_scaffold_4-snap.2781-T1
Couldn't classify 104452, 104732
Sorry, prediction pasa_asmbl_43606.p1 fails validation.
(CTT)	 AA	104452-104732	GT	AAG
(AAA)	 AG	105753-105826	GT	TGG
(GCT)	 AG	106425-106669	GT	AGG
(GCG)	 AG	107296-107486	GT	AGG
(GCG)	 AG	107572-107707	GT	AGG
(GTG)	 AG	107872-108013	GT	AGG
(CTG)	 AG	108203-108345	GG	GAG
-recovered pasa_asmbl_43606.p1, terminal, 108203, 108345
-recovered pasa_asmbl_43606.p1, internal, 105753, 105826
-recovered pasa_asmbl_43606.p1, internal, 106425, 106669
-recovered pasa_asmbl_43606.p1, internal, 107296, 107486
-recovered pasa_asmbl_43606.p1, internal, 107572, 107707
-recovered pasa_asmbl_43606.p1, internal, 107872, 108013
Valid prediction for GlimmerHMM_glimmerT_10465-T1
Valid prediction for snap_scaffold_4-snap.2769-T1
Valid prediction for HiQ_model.g6847.t1
Valid prediction for snap_scaffold_4-snap.2773-T1
Valid prediction for GlimmerHMM_glimmerT_10460-T1
Valid prediction for GlimmerHMM_glimmerT_10477-T1
Valid prediction for snap_scaffold_4-snap.2787-T1
Valid prediction for CodingQuarry_transcript_49182-T1
Valid prediction for GlimmerHMM_glimmerT_10479-T1
Couldn't classify 88678, 88752
Sorry, prediction pasa_asmbl_42997.p1 fails validation.
(TTG)	 TG	88678-88752	GT	TGG
(TCC)	 AG	88865-89031	GT	AGG
(ATT)	 AG	89171-89227	GT	AGG
(AGC)	 AG	89333-89526	GT	AGG
(ATA)	 AG	89818-89927	GT	CTG
(GAG)	 AG	90094-90309	GT	AGG
(GAG)	 AG	90759-90862	GT	AAG
(GGA)	 AG	90996-91080	GT	AGG
(GAG)	 AG	91751-91810	GT	GGG
(TCC)	 AG	92213-92299	GT	AGG
(AAT)	 AG	92421-92453	GT	GTG
(GAG)	 AG	92693-92814	GC	AGG
(TTA)	 AG	92933-93022	GT	GAG
(CTT)	 AG	93145-93238	GT	AGG
(CAT)	 AG	93530-93760	GT	TGG
(GTG)	 AG	93970-94084	GT	AGG
(AGT)	 AG	94184-94365	CA	GAC
-recovered pasa_asmbl_42997.p1, terminal, 94184, 94365
-recovered pasa_asmbl_42997.p1, internal, 88865, 89031
-recovered pasa_asmbl_42997.p1, internal, 89171, 89227
-recovered pasa_asmbl_42997.p1, internal, 89333, 89526
-recovered pasa_asmbl_42997.p1, internal, 89818, 89927
-recovered pasa_asmbl_42997.p1, internal, 90094, 90309
-recovered pasa_asmbl_42997.p1, internal, 90759, 90862
-recovered pasa_asmbl_42997.p1, internal, 90996, 91080
-recovered pasa_asmbl_42997.p1, internal, 91751, 91810
-recovered pasa_asmbl_42997.p1, internal, 92213, 92299
-recovered pasa_asmbl_42997.p1, internal, 92421, 92453
-recovered pasa_asmbl_42997.p1, internal, 92693, 92814
-recovered pasa_asmbl_42997.p1, internal, 92933, 93022
-recovered pasa_asmbl_42997.p1, internal, 93145, 93238
-recovered pasa_asmbl_42997.p1, internal, 93530, 93760
-recovered pasa_asmbl_42997.p1, internal, 93970, 94084
Valid prediction for snap_scaffold_4-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_10478-T1
Valid prediction for snap_scaffold_4-snap.2759-T1
Couldn't classify 116386, 116481
Couldn't classify 119881, 120003
Sorry, prediction pasa_asmbl_42995.p1 fails validation.
(CAT)	 CG	116386-116481	GT	AGG
(GAA)	 AG	116674-117006	GT	GGG
(CTT)	 AG	117290-117479	GT	TGG
(GTG)	 AG	117570-117684	GT	AGG
(TGC)	 AG	117832-117962	GT	AGG
(GGG)	 AG	118114-118319	GT	AGG
(GCA)	 AG	118479-118676	GT	GCG
(ATG)	 AG	118849-118977	GT	AGG
(GTT)	 AG	119069-119269	GT	AGG
(AAT)	 AG	119421-119594	GT	AGG
(ATC)	 AG	119881-120003	AA	ACA
-recovered pasa_asmbl_42995.p1, initial, 118849, 118977
-recovered pasa_asmbl_42995.p1, internal, 116674, 117006
-recovered pasa_asmbl_42995.p1, internal, 117290, 117479
-recovered pasa_asmbl_42995.p1, internal, 117570, 117684
-recovered pasa_asmbl_42995.p1, internal, 117832, 117962
-recovered pasa_asmbl_42995.p1, internal, 118114, 118319
-recovered pasa_asmbl_42995.p1, internal, 118479, 118676
-recovered pasa_asmbl_42995.p1, internal, 118849, 118977
-recovered pasa_asmbl_42995.p1, internal, 119069, 119269
-recovered pasa_asmbl_42995.p1, internal, 119421, 119594
Valid prediction for snap_scaffold_4-snap.2761-T1
Valid prediction for pasa_asmbl_42983.p1
Valid prediction for Augustus_model.g6845.t1
Valid prediction for GlimmerHMM_glimmerT_10481-T1
Valid prediction for Augustus_model.g6846.t1
Valid prediction for GlimmerHMM_glimmerT_10487-T1
Valid prediction for HiQ_model.g6833.t1
Valid prediction for GlimmerHMM_glimmerT_10483-T1
Valid prediction for pasa_asmbl_42980.p1
Couldn't classify 124775, 124912
Couldn't classify 125393, 125544
Sorry, prediction pasa_asmbl_42993.p1 fails validation.
(GAT)	 AG	124775-124912	GT	AGG
(CCC)	 AG	125135-125282	GT	CGG
(CTG)	 AG	125393-125544	CC	AGC
-recovered pasa_asmbl_42993.p1, internal, 124775, 124912
-recovered pasa_asmbl_42993.p1, internal, 125135, 125282
Valid prediction for HiQ_model.g6851.t1
Couldn't classify 126133, 126240
Sorry, prediction pasa_asmbl_43491.p1 fails validation.
(CAC)	 AG	126133-126240	GT	AGG
(AGG)	 AG	126369-126497	GT	AGG
(GAT)	 AG	126773-127006	GT	AGG
(CTC)	 AG	127198-127472	GT	AAG
(GAC)	 AG	127788-128110	GT	TGG
(TGA)	 AG	128202-128327	GT	AGG
(TTG)	 AG	128429-128553	GC	GAG
-recovered pasa_asmbl_43491.p1, terminal, 128429, 128553
-recovered pasa_asmbl_43491.p1, internal, 126133, 126240
-recovered pasa_asmbl_43491.p1, internal, 126369, 126497
-recovered pasa_asmbl_43491.p1, internal, 126773, 127006
-recovered pasa_asmbl_43491.p1, internal, 127198, 127472
-recovered pasa_asmbl_43491.p1, internal, 127788, 128110
-recovered pasa_asmbl_43491.p1, internal, 128202, 128327
-recovered pasa_asmbl_43491.p1, internal, 128429, 128553
Valid prediction for snap_scaffold_4-snap.2788-T1
Couldn't classify 120122, 120253
Sorry, prediction pasa_asmbl_42994.p1 fails validation.
(GGG)	 CG	120122-120253	GT	TGG
(GTG)	 AG	120387-120620	AC	AGA
-recovered pasa_asmbl_42994.p1, terminal, 120387, 120620
Valid prediction for Augustus_model.g6840.t1
Valid prediction for snap_scaffold_4-snap.2757-T1
Valid prediction for snap_scaffold_4-snap.2784-T1
Valid prediction for snap_scaffold_4-snap.2772-T1
Valid prediction for snap_scaffold_4-snap.2782-T1
Valid prediction for snap_scaffold_4-snap.2770-T1
Valid prediction for CodingQuarry_transcript_49195-T1
Valid prediction for CodingQuarry_transcript_49183-T1
Valid prediction for Augustus_model.g6849.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 99437, rend_intergenic: 94944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285874, rend_intergenic: 284185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 395663
-exon list size: 393


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 99437, rend_intergenic: 94944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285874, rend_intergenic: 284185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 38653
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 32318
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12812
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2087 - 12812

-building DP trellis

-building trellis in range 12860 - 32318
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 20579 - 32318
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support