-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_14684312-14864131

-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_2-snap.2800-T1
Valid prediction for snap_scaffold_2-snap.2829-T1
Valid prediction for snap_scaffold_2-snap.2832-T1
Valid prediction for snap_scaffold_2-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_4955-T1
Valid prediction for snap_scaffold_2-snap.2812-T1
Couldn't classify 40241, 40285
Couldn't classify 41330, 41479
Sorry, prediction pasa_asmbl_25414.p1 fails validation.
(GCC)	 CA	40241-40285	GT	AGG
(CCT)	 AG	40547-40639	GT	AGG
(GAG)	 AG	41038-41148	GT	AGG
(TCT)	 AG	41330-41479	AG	ACA
-recovered pasa_asmbl_25414.p1, internal, 40547, 40639
-recovered pasa_asmbl_25414.p1, internal, 41038, 41148
Valid prediction for Augustus_model.g3346.t1
Valid prediction for GlimmerHMM_glimmerT_4952-T1
Valid prediction for snap_scaffold_2-snap.2805-T1
Valid prediction for GlimmerHMM_glimmerT_4960-T1
Valid prediction for Augustus_model.g3341.t1
Couldn't classify 29358, 29565
Couldn't classify 32287, 32457
Sorry, prediction pasa_asmbl_24970.p1 fails validation.
(TGT)	 AG	29358-29565	GT	CAG
(GTA)	 AG	29662-29778	GT	GAG
(GGA)	 AG	29890-29991	GT	AGG
(GGT)	 AG	30496-30651	GT	TGG
(GAA)	 AG	31059-31159	GT	ACG
(GAC)	 AG	32287-32457	AT	GCA
-recovered pasa_asmbl_24970.p1, internal, 29358, 29565
-recovered pasa_asmbl_24970.p1, internal, 29662, 29778
-recovered pasa_asmbl_24970.p1, internal, 29890, 29991
-recovered pasa_asmbl_24970.p1, internal, 30496, 30651
-recovered pasa_asmbl_24970.p1, internal, 31059, 31159
Valid prediction for snap_scaffold_2-snap.2835-T1
Valid prediction for snap_scaffold_2-snap.2830-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2821-T1
Valid prediction for Augustus_model.g3340.t1
Valid prediction for snap_scaffold_2-snap.2815-T1
Valid prediction for snap_scaffold_2-snap.2827-T1
Valid prediction for Augustus_model.g3347.t1
Valid prediction for GlimmerHMM_glimmerT_4954-T1
Valid prediction for pasa_asmbl_24974.p1
Couldn't classify 38241, 38246
Sorry, prediction pasa_asmbl_24971.p1 fails validation.
(ATG)	 CT	32675-32778	GT	AGG
(GGA)	 AG	33081-33207	GT	AGG
(GTA)	 AG	33309-33402	GT	CGG
(ACC)	 AG	33650-33679	GT	AGG
(AGT)	 AG	34257-34404	GT	ATG
(TGA)	 AG	35251-35447	GT	AGG
(AAA)	 AG	35644-35762	GT	AGG
(GAC)	 AG	35970-36041	GT	ACG
(GAT)	 AG	36174-36350	GT	AGG
(GGA)	 AG	37673-37774	GT	AGG
(AAA)	 AG	38241-38246	AC	GCA
-recovered pasa_asmbl_24971.p1, initial, 32675, 32778
-recovered pasa_asmbl_24971.p1, internal, 33081, 33207
-recovered pasa_asmbl_24971.p1, internal, 33309, 33402
-recovered pasa_asmbl_24971.p1, internal, 33650, 33679
-recovered pasa_asmbl_24971.p1, internal, 34257, 34404
-recovered pasa_asmbl_24971.p1, internal, 35251, 35447
-recovered pasa_asmbl_24971.p1, internal, 35644, 35762
-recovered pasa_asmbl_24971.p1, internal, 35970, 36041
-recovered pasa_asmbl_24971.p1, internal, 36174, 36350
-recovered pasa_asmbl_24971.p1, internal, 37673, 37774
Valid prediction for snap_scaffold_2-snap.2834-T1
Valid prediction for snap_scaffold_2-snap.2802-T1
Valid prediction for CodingQuarry_transcript_28746-T1
Valid prediction for snap_scaffold_2-snap.2807-T1
Valid prediction for snap_scaffold_2-snap.2806-T1
Valid prediction for snap_scaffold_2-snap.2824-T1
Valid prediction for GlimmerHMM_glimmerT_4950-T1
Valid prediction for snap_scaffold_2-snap.2825-T1
Valid prediction for snap_scaffold_2-snap.2816-T1
Valid prediction for Augustus_model.g3351.t1
Valid prediction for snap_scaffold_2-snap.2809-T1
Valid prediction for GlimmerHMM_glimmerT_4961-T1
Valid prediction for snap_scaffold_2-snap.2810-T1
Valid prediction for GlimmerHMM_glimmerT_4972-T1
Valid prediction for snap_scaffold_2-snap.2833-T1
Valid prediction for Augustus_model.g3350.t1
Valid prediction for pasa_asmbl_24982.p1
Valid prediction for GlimmerHMM_glimmerT_4951-T1
Valid prediction for snap_scaffold_2-snap.2803-T1
Valid prediction for GlimmerHMM_glimmerT_4970-T1
Valid prediction for snap_scaffold_2-snap.2819-T1
Couldn't classify 64134, 64342
Sorry, prediction pasa_asmbl_24975.p1 fails validation.
(CTG)	 TC	64134-64342	GT	TTG
(TGC)	 AG	64528-64601	GT	AGG
(ACC)	 AG	64710-64894	GG	GAG
-recovered pasa_asmbl_24975.p1, terminal, 64710, 64894
-recovered pasa_asmbl_24975.p1, internal, 64528, 64601
Couldn't classify 43022, 43108
Couldn't classify 44644, 44757
Sorry, prediction pasa_asmbl_24972.p1 fails validation.
(AGC)	 TG	43022-43108	GT	TGG
(GGC)	 AG	43548-43734	GT	CGG
(GGA)	 AG	44299-44393	GT	AGG
(GAC)	 AG	44644-44757	TT	CCT
-recovered pasa_asmbl_24972.p1, internal, 43548, 43734
-recovered pasa_asmbl_24972.p1, internal, 44299, 44393
Valid prediction for GlimmerHMM_glimmerT_4948-T1
Valid prediction for HiQ_model.g3342.t1
Valid prediction for GlimmerHMM_glimmerT_4963-T1
Valid prediction for GlimmerHMM_glimmerT_4959-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.g3349.t1
Valid prediction for snap_scaffold_2-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_4969-T1
Valid prediction for snap_scaffold_2-snap.2823-T1
Valid prediction for GlimmerHMM_glimmerT_4967-T1
Valid prediction for GlimmerHMM_glimmerT_4958-T1
Couldn't classify 90802, 90903
Sorry, prediction pasa_asmbl_23612.p1 fails validation.
(GTC)	 AG	90802-90903	GT	AGG
(TGG)	 AG	91299-91430	GT	GGG
(GGC)	 AG	92570-92653	GT	AGG
(CTC)	 AG	94047-94118	CG	AGC
-recovered pasa_asmbl_23612.p1, terminal, 94047, 94118
-recovered pasa_asmbl_23612.p1, internal, 90802, 90903
-recovered pasa_asmbl_23612.p1, internal, 91299, 91430
-recovered pasa_asmbl_23612.p1, internal, 92570, 92653
Valid prediction for snap_scaffold_2-snap.2798-T1
Valid prediction for GlimmerHMM_glimmerT_4957-T1
Valid prediction for Augustus_model.g3343.t1
Valid prediction for Augustus_model.g3345.t1
Valid prediction for Augustus_model.g3344.t1
Valid prediction for snap_scaffold_2-snap.2813-T1
Valid prediction for GlimmerHMM_glimmerT_4971-T1
Valid prediction for GlimmerHMM_glimmerT_4966-T1
Valid prediction for snap_scaffold_2-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_4956-T1
Valid prediction for GlimmerHMM_glimmerT_4962-T1
Valid prediction for GlimmerHMM_glimmerT_4953-T1
Valid prediction for snap_scaffold_2-snap.2826-T1
Valid prediction for Augustus_model.g3339.t1
Valid prediction for CodingQuarry_transcript_28747-T1
Valid prediction for snap_scaffold_2-snap.2817-T1
Valid prediction for GlimmerHMM_glimmerT_4968-T1
Valid prediction for snap_scaffold_2-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_4965-T1
Valid prediction for snap_scaffold_2-snap.2804-T1
Valid prediction for snap_scaffold_2-snap.2808-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_4964-T1
Valid prediction for GlimmerHMM_glimmerT_4949-T1
Valid prediction for Augustus_model.g3348.t1
Valid prediction for snap_scaffold_2-snap.2818-T1
Valid prediction for snap_scaffold_2-snap.2814-T1
Valid prediction for snap_scaffold_2-snap.2822-T1
Valid prediction for snap_scaffold_2-snap.2820-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41520, rend_intergenic: 38699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62209, rend_intergenic: 61502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65502, rend_intergenic: 62475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72017, rend_intergenic: 70379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90225, rend_intergenic: 83833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106407, rend_intergenic: 102537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117760, rend_intergenic: 113138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142447, rend_intergenic: 138717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144778, rend_intergenic: 142704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179820
-exon list size: 319


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 41520, rend_intergenic: 38699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62209, rend_intergenic: 61502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65502, rend_intergenic: 62475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72017, rend_intergenic: 70379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90225, rend_intergenic: 83833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106407, rend_intergenic: 102537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117760, rend_intergenic: 113138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142447, rend_intergenic: 138717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144778, rend_intergenic: 142704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support