-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_15956379-16102008

-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 GeneMark_model.8477_t
Valid prediction for GlimmerHMM_glimmerT_5307-T1
Valid prediction for snap_scaffold_2-snap.3088-T1
Valid prediction for GeneMark_model.8472_t
Valid prediction for GeneMark_model.8463_t
Valid prediction for GlimmerHMM_glimmerT_5302-T1
Valid prediction for Augustus_model.g3591.t1
Valid prediction for pasa_asmbl_25121.p1
Valid prediction for snap_scaffold_2-snap.3100-T1
Valid prediction for GlimmerHMM_glimmerT_5289-T1
Valid prediction for GeneMark_model.8452_t
Valid prediction for GeneMark_model.8444_t
Valid prediction for GeneMark_model.8464_t
Valid prediction for GlimmerHMM_glimmerT_5300-T1
Valid prediction for GlimmerHMM_glimmerT_5283-T1
Valid prediction for GeneMark_model.8448_t
Couldn't classify 41548, 41641
Sorry, prediction pasa_asmbl_25115.p1 fails validation.
(CCC)	 CC	41548-41641	GT	GGG
(CTG)	 AG	41799-41968	GT	TGG
(GGA)	 AG	42081-42154	GT	CCG
(GGC)	 AG	42235-42484	GT	TGG
(AAT)	 AG	42611-42858	GT	AGG
(GCA)	 AG	43013-43160	GT	AGG
(ATC)	 AG	43242-43392	GT	CGG
(GTA)	 AG	43535-43611	GT	AGG
(TCC)	 AG	43922-44029	AT	AGA
-recovered pasa_asmbl_25115.p1, terminal, 43922, 44029
-recovered pasa_asmbl_25115.p1, internal, 41799, 41968
-recovered pasa_asmbl_25115.p1, internal, 42081, 42154
-recovered pasa_asmbl_25115.p1, internal, 42235, 42484
-recovered pasa_asmbl_25115.p1, internal, 42611, 42858
-recovered pasa_asmbl_25115.p1, internal, 43013, 43160
-recovered pasa_asmbl_25115.p1, internal, 43242, 43392
-recovered pasa_asmbl_25115.p1, internal, 43535, 43611
Valid prediction for GeneMark_model.8450_t
Valid prediction for snap_scaffold_2-snap.3106-T1
Valid prediction for GeneMark_model.8442_t
Valid prediction for CodingQuarry_transcript_28732-T1
Valid prediction for GeneMark_model.8471_t
Valid prediction for GeneMark_model.8469_t
Valid prediction for pasa_asmbl_25123.p1
Valid prediction for snap_scaffold_2-snap.3115-T1
Valid prediction for Augustus_model.g3578.t1
Valid prediction for Augustus_model.g3569.t1
Valid prediction for GlimmerHMM_glimmerT_5294-T1
Valid prediction for GlimmerHMM_glimmerT_5299-T1
Valid prediction for GeneMark_model.8449_t
Valid prediction for Augustus_model.g3587.t1
Valid prediction for snap_scaffold_2-snap.3089-T1
Valid prediction for GlimmerHMM_glimmerT_5282-T1
Valid prediction for GeneMark_model.8459_t
Valid prediction for GeneMark_model.8475_t
Valid prediction for HiQ_model.g3574.t1
Valid prediction for snap_scaffold_2-snap.3086-T1
Valid prediction for Augustus_model.g3570.t1
Valid prediction for pasa_asmbl_25118.p1
Valid prediction for GeneMark_model.8465_t
Valid prediction for snap_scaffold_2-snap.3101-T1
Valid prediction for CodingQuarry_transcript_28734-T1
Valid prediction for HiQ_model.g3584.t1
Valid prediction for GeneMark_model.8476_t
Valid prediction for GeneMark_model.8446_t
Valid prediction for GeneMark_model.8467_t
Valid prediction for HiQ_model.g3581.t1
Valid prediction for Augustus_model.g3579.t1
Valid prediction for GlimmerHMM_glimmerT_5280-T1
Valid prediction for snap_scaffold_2-snap.3095-T1
Valid prediction for Augustus_model.g3585.t1
Valid prediction for GlimmerHMM_glimmerT_5286-T1
Valid prediction for GlimmerHMM_glimmerT_5279-T1
Valid prediction for Augustus_model.g3583.t1
Valid prediction for GeneMark_model.8454_t
Valid prediction for snap_scaffold_2-snap.3110-T1
Valid prediction for GlimmerHMM_glimmerT_5296-T1
Valid prediction for Augustus_model.g3573.t1
Valid prediction for snap_scaffold_2-snap.3098-T1
Valid prediction for GeneMark_model.8451_t
Valid prediction for CodingQuarry_transcript_28733-T1
Valid prediction for GlimmerHMM_glimmerT_5303-T1
Valid prediction for GeneMark_model.8461_t
Valid prediction for snap_scaffold_2-snap.3112-T1
Valid prediction for snap_scaffold_2-snap.3093-T1
Valid prediction for snap_scaffold_2-snap.3107-T1
Valid prediction for GeneMark_model.8456_t
Valid prediction for Augustus_model.g3571.t1
Valid prediction for snap_scaffold_2-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_5298-T1
Valid prediction for snap_scaffold_2-snap.3105-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_2-snap.3094-T1
Valid prediction for GeneMark_model.8445_t
Valid prediction for snap_scaffold_2-snap.3092-T1
Valid prediction for snap_scaffold_2-snap.3087-T1
Valid prediction for snap_scaffold_2-snap.3102-T1
Valid prediction for Augustus_model.g3580.t1
Valid prediction for GeneMark_model.8453_t
Valid prediction for GlimmerHMM_glimmerT_5292-T1
Valid prediction for GlimmerHMM_glimmerT_5293-T1
Valid prediction for pasa_asmbl_23688.p1
Valid prediction for CodingQuarry_transcript_28737-T1
Couldn't classify 41008, 41337
Sorry, prediction pasa_asmbl_24074.p1 fails validation.
(ATG)	 TC	40460-40562	GC	AGG
(AGG)	 AG	40752-40831	GT	AGG
(CTT)	 AG	41008-41337	TT	CCT
-recovered pasa_asmbl_24074.p1, initial, 40460, 40562
-recovered pasa_asmbl_24074.p1, internal, 40752, 40831
Valid prediction for GeneMark_model.8479_t
Valid prediction for GlimmerHMM_glimmerT_5305-T1
Valid prediction for GlimmerHMM_glimmerT_5290-T1
Valid prediction for snap_scaffold_2-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_5284-T1
Valid prediction for GlimmerHMM_glimmerT_5287-T1
Valid prediction for GlimmerHMM_glimmerT_5301-T1
Valid prediction for snap_scaffold_2-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_5285-T1
Valid prediction for GlimmerHMM_glimmerT_5304-T1
Valid prediction for GeneMark_model.8455_t
Valid prediction for GlimmerHMM_glimmerT_5306-T1
Valid prediction for GeneMark_model.8468_t
Valid prediction for HiQ_model.g3590.t1
Valid prediction for Augustus_model.g3576.t1
Valid prediction for GeneMark_model.8466_t
Valid prediction for GeneMark_model.8480_t
Valid prediction for snap_scaffold_2-snap.3111-T1
Valid prediction for GeneMark_model.8473_t
Valid prediction for snap_scaffold_2-snap.3097-T1
Valid prediction for snap_scaffold_2-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_5281-T1
Valid prediction for HiQ_model.g3586.t1
Valid prediction for Augustus_model.g3589.t1
Valid prediction for Augustus_model.g3588.t1
Couldn't classify 23027, 23202
Sorry, prediction pasa_asmbl_24024.p1 fails validation.
(GAC)	 AT	23027-23202	GT	AAG
(AGC)	 AG	23301-23395	GT	CAG
(GTG)	 AG	23552-23715	GT	AGG
(GTC)	 AG	23912-24112	GT	TTG
(ACG)	 AG	24236-24383	GT	AGG
(GTG)	 AG	24489-24663	GT	ACG
(AGC)	 AG	24765-24947	GT	AAG
(GGA)	 AG	25183-25301	GT	GGG
(GTG)	 AG	25458-25552	GT	AGG
(GTC)	 AG	25647-25770	GT	AGG
(GCG)	 AG	25859-26701	GT	AGG
(GGA)	 AG	26811-27010	GT	AGG
(GTT)	 AG	27111-27305	CA	GAC
-recovered pasa_asmbl_24024.p1, terminal, 27111, 27305
-recovered pasa_asmbl_24024.p1, internal, 23301, 23395
-recovered pasa_asmbl_24024.p1, internal, 23552, 23715
-recovered pasa_asmbl_24024.p1, internal, 23912, 24112
-recovered pasa_asmbl_24024.p1, internal, 24236, 24383
-recovered pasa_asmbl_24024.p1, internal, 24489, 24663
-recovered pasa_asmbl_24024.p1, internal, 24765, 24947
-recovered pasa_asmbl_24024.p1, internal, 25183, 25301
-recovered pasa_asmbl_24024.p1, internal, 25458, 25552
-recovered pasa_asmbl_24024.p1, internal, 25647, 25770
-recovered pasa_asmbl_24024.p1, internal, 25859, 26701
-recovered pasa_asmbl_24024.p1, internal, 26811, 27010
Valid prediction for GlimmerHMM_glimmerT_5295-T1
Valid prediction for snap_scaffold_2-snap.3103-T1
Valid prediction for GeneMark_model.8458_t
Valid prediction for Augustus_model.g3572.t1
Couldn't classify 9602, 9632
Sorry, prediction pasa_asmbl_23977.p1 fails validation.
(CAA)	 GC	9602-9632	GT	GGG
(GCT)	 AG	9713-9794	GT	AGG
(GTT)	 AG	9896-10010	GT	AGG
(GAG)	 AG	10347-10454	GT	AGG
(CAG)	 AG	10573-10649	GT	GGG
(GTT)	 AG	10749-10836	GA	AAG
-recovered pasa_asmbl_23977.p1, terminal, 10749, 10836
-recovered pasa_asmbl_23977.p1, internal, 9713, 9794
-recovered pasa_asmbl_23977.p1, internal, 9896, 10010
-recovered pasa_asmbl_23977.p1, internal, 10347, 10454
-recovered pasa_asmbl_23977.p1, internal, 10573, 10649
Valid prediction for snap_scaffold_2-snap.3099-T1
Valid prediction for CodingQuarry_transcript_28736-T1
Valid prediction for GeneMark_model.8460_t
Valid prediction for GeneMark_model.8470_t
Valid prediction for pasa_asmbl_23682.p1
Valid prediction for HiQ_model.g3582.t1
Valid prediction for GlimmerHMM_glimmerT_5288-T1
Valid prediction for Augustus_model.g3577.t1
Valid prediction for CodingQuarry_transcript_28735-T1
Valid prediction for GeneMark_model.8457_t
Valid prediction for GlimmerHMM_glimmerT_5291-T1
Couldn't classify 49572, 49736
Sorry, prediction pasa_asmbl_24020.p1 fails validation.
(ATG)	 TG	48762-48786	GT	TGG
(CCA)	 AG	49220-49386	GT	AGG
(ATC)	 AG	49572-49736	AA	AGA
-recovered pasa_asmbl_24020.p1, initial, 48762, 48786
-recovered pasa_asmbl_24020.p1, internal, 49220, 49386
Valid prediction for snap_scaffold_2-snap.3091-T1
Valid prediction for snap_scaffold_2-snap.3096-T1
Valid prediction for snap_scaffold_2-snap.3104-T1
Valid prediction for GeneMark_model.8447_t
Valid prediction for snap_scaffold_2-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_5297-T1
Valid prediction for GeneMark_model.8462_t
Valid prediction for Augustus_model.g3575.t1
Valid prediction for GeneMark_model.8443_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13530, rend_intergenic: 12271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44276, rend_intergenic: 34888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76973, rend_intergenic: 70133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145630
-exon list size: 545


building trellis

0.2    
0.4    
0.5    
0.7    
0.9    
1.1    
1.3    
1.5    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.7    
17.9    
18.1    
18.3    
18.5    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.0    
23.2    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.4    
46.6    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 13530, rend_intergenic: 12271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44276, rend_intergenic: 34888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76973, rend_intergenic: 70133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support