-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_16780828-16947321

-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.3232-T1
Valid prediction for GlimmerHMM_glimmerT_5295-T1
Valid prediction for GlimmerHMM_glimmerT_5297-T1
Valid prediction for snap_scaffold_2-snap.3248-T1
Valid prediction for GlimmerHMM_glimmerT_5309-T1
Valid prediction for GlimmerHMM_glimmerT_5298-T1
Valid prediction for snap_scaffold_2-snap.3261-T1
Valid prediction for snap_scaffold_2-snap.3259-T1
Valid prediction for GlimmerHMM_glimmerT_5293-T1
Valid prediction for CodingQuarry_transcript_28804-T1
Valid prediction for snap_scaffold_2-snap.3251-T1
Valid prediction for snap_scaffold_2-snap.3228-T1
Valid prediction for GlimmerHMM_glimmerT_5303-T1
Valid prediction for snap_scaffold_2-snap.3242-T1
Valid prediction for Augustus_model.g3575.t1
Valid prediction for Augustus_model.g3577.t1
Valid prediction for Augustus_model.g3573.t1
Valid prediction for GlimmerHMM_glimmerT_5294-T1
Couldn't classify 64160, 64396
Couldn't classify 67927, 67974
Sorry, prediction pasa_asmbl_25145.p1 fails validation.
(GCA)	 AG	64160-64396	GT	AGG
(TAT)	 AG	65053-65136	GT	CGG
(CCT)	 AG	66438-66557	GT	AGG
(AAC)	 AG	67927-67974	AA	ACA
-recovered pasa_asmbl_25145.p1, internal, 64160, 64396
-recovered pasa_asmbl_25145.p1, internal, 65053, 65136
-recovered pasa_asmbl_25145.p1, internal, 66438, 66557
Valid prediction for snap_scaffold_2-snap.3239-T1
Couldn't classify 55566, 55661
Couldn't classify 63922, 63994
Sorry, prediction pasa_asmbl_25144.p1 fails validation.
(GAG)	 AG	55566-55661	GT	AGG
(GCC)	 AG	58020-58135	GT	AGG
(GTT)	 AG	60693-61187	GT	AGG
(CAT)	 AG	63922-63994	GG	AGG
-recovered pasa_asmbl_25144.p1, internal, 55566, 55661
-recovered pasa_asmbl_25144.p1, internal, 58020, 58135
-recovered pasa_asmbl_25144.p1, internal, 60693, 61187
Valid prediction for GlimmerHMM_glimmerT_5296-T1
Couldn't classify 83480, 83653
Couldn't classify 86839, 86903
Sorry, prediction pasa_asmbl_25153.p1 fails validation.
(GGC)	 GT	83480-83653	GT	GGG
(GTG)	 AG	84224-84331	GT	AGG
(TGT)	 AG	84956-85142	GT	ACG
(TCT)	 AG	86839-86903	CA	GCC
-recovered pasa_asmbl_25153.p1, internal, 84224, 84331
-recovered pasa_asmbl_25153.p1, internal, 84956, 85142
Valid prediction for GlimmerHMM_glimmerT_5301-T1
Couldn't classify 54040, 54140
Sorry, prediction pasa_asmbl_25143.p2 fails validation.
(ATG)	 CC	48476-48544	GT	GGG
(CCT)	 AG	48686-48790	GT	AGG
(GAC)	 AG	51763-51835	GT	AGG
(ATG)	 AG	54040-54140	GT	AGG
-recovered pasa_asmbl_25143.p2, initial, 48476, 48544
-recovered pasa_asmbl_25143.p2, initial, 54040, 54140
-recovered pasa_asmbl_25143.p2, internal, 48686, 48790
-recovered pasa_asmbl_25143.p2, internal, 51763, 51835
-recovered pasa_asmbl_25143.p2, internal, 54040, 54140
Valid prediction for snap_scaffold_2-snap.3226-T1
Valid prediction for snap_scaffold_2-snap.3229-T1
Valid prediction for snap_scaffold_2-snap.3240-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3249-T1
Valid prediction for snap_scaffold_2-snap.3264-T1
Valid prediction for snap_scaffold_2-snap.3234-T1
Valid prediction for GlimmerHMM_glimmerT_5310-T1
Valid prediction for snap_scaffold_2-snap.3236-T1
Valid prediction for Augustus_model.g3579.t1
Valid prediction for GlimmerHMM_glimmerT_5290-T1
Valid prediction for Augustus_model.g3581.t1
Valid prediction for snap_scaffold_2-snap.3245-T1
Valid prediction for snap_scaffold_2-snap.3230-T1
Valid prediction for GlimmerHMM_glimmerT_5307-T1
Couldn't classify 72192, 72257
Sorry, prediction pasa_asmbl_25146.p1 fails validation.
(CAG)	 TC	72192-72257	GT	ACG
(GCC)	 AG	72809-72889	GT	AGG
(CAC)	 AG	72984-73133	GT	CTG
(GAG)	 AG	73308-73409	GT	AGG
(ACA)	 AG	74594-74791	GT	AGG
(GGT)	 AG	77002-77119	GT	AGG
(GAA)	 AG	77406-77521	GT	CGG
(GAG)	 AG	77836-78060	GT	AGG
(GCC)	 AG	78456-78617	GT	AGG
(CTG)	 AG	79078-79211	GT	AGG
(CAT)	 AG	79868-80007	GT	AGG
(TGC)	 AG	80292-80398	TA	AGT
-recovered pasa_asmbl_25146.p1, terminal, 80292, 80398
-recovered pasa_asmbl_25146.p1, internal, 72809, 72889
-recovered pasa_asmbl_25146.p1, internal, 72984, 73133
-recovered pasa_asmbl_25146.p1, internal, 73308, 73409
-recovered pasa_asmbl_25146.p1, internal, 74594, 74791
-recovered pasa_asmbl_25146.p1, internal, 77002, 77119
-recovered pasa_asmbl_25146.p1, internal, 77406, 77521
-recovered pasa_asmbl_25146.p1, internal, 77836, 78060
-recovered pasa_asmbl_25146.p1, internal, 78456, 78617
-recovered pasa_asmbl_25146.p1, internal, 79078, 79211
-recovered pasa_asmbl_25146.p1, internal, 79868, 80007
Valid prediction for snap_scaffold_2-snap.3253-T1
Valid prediction for Augustus_model.g3578.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_5287-T1
Valid prediction for snap_scaffold_2-snap.3233-T1
Valid prediction for snap_scaffold_2-snap.3254-T1
Valid prediction for Augustus_model.g3580.t1
Valid prediction for GlimmerHMM_glimmerT_5285-T1
Valid prediction for snap_scaffold_2-snap.3262-T1
Valid prediction for snap_scaffold_2-snap.3227-T1
Valid prediction for snap_scaffold_2-snap.3231-T1
Valid prediction for snap_scaffold_2-snap.3252-T1
Valid prediction for snap_scaffold_2-snap.3255-T1
Valid prediction for snap_scaffold_2-snap.3241-T1
Valid prediction for GlimmerHMM_glimmerT_5288-T1
Valid prediction for GlimmerHMM_glimmerT_5300-T1
Valid prediction for GlimmerHMM_glimmerT_5286-T1
Valid prediction for GlimmerHMM_glimmerT_5299-T1
Valid prediction for Augustus_model.g3576.t1
Valid prediction for snap_scaffold_2-snap.3246-T1
Valid prediction for snap_scaffold_2-snap.3235-T1
Valid prediction for GlimmerHMM_glimmerT_5302-T1
Valid prediction for snap_scaffold_2-snap.3247-T1
Valid prediction for GlimmerHMM_glimmerT_5306-T1
Valid prediction for snap_scaffold_2-snap.3237-T1
Valid prediction for Augustus_model.g3574.t1
Valid prediction for snap_scaffold_2-snap.3263-T1
Valid prediction for Augustus_model.g3582.t1
Valid prediction for snap_scaffold_2-snap.3260-T1
Valid prediction for Augustus_model.g3583.t1
Valid prediction for GlimmerHMM_glimmerT_5305-T1
Valid prediction for GlimmerHMM_glimmerT_5308-T1
Valid prediction for GlimmerHMM_glimmerT_5292-T1
Valid prediction for snap_scaffold_2-snap.3256-T1
Valid prediction for GlimmerHMM_glimmerT_5289-T1
Valid prediction for snap_scaffold_2-snap.3238-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5291-T1
Valid prediction for snap_scaffold_2-snap.3250-T1
Valid prediction for snap_scaffold_2-snap.3243-T1
Valid prediction for snap_scaffold_2-snap.3258-T1
Valid prediction for snap_scaffold_2-snap.3257-T1
Valid prediction for GlimmerHMM_glimmerT_5304-T1
Valid prediction for snap_scaffold_2-snap.3244-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18647, rend_intergenic: 12333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46643, rend_intergenic: 42716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49668, rend_intergenic: 48950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60294, rend_intergenic: 52539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66979, rend_intergenic: 61571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75598, rend_intergenic: 66993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80881, rend_intergenic: 75751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91099, rend_intergenic: 83311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99947, rend_intergenic: 97391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102441, rend_intergenic: 100919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108825, rend_intergenic: 104937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119467, rend_intergenic: 109141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123147, rend_intergenic: 121420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145828, rend_intergenic: 143827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149797, rend_intergenic: 146093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158249, rend_intergenic: 151420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166494
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 18647, rend_intergenic: 12333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46643, rend_intergenic: 42716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49668, rend_intergenic: 48950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60294, rend_intergenic: 52539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66979, rend_intergenic: 61571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75598, rend_intergenic: 66993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80881, rend_intergenic: 75751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91099, rend_intergenic: 83311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99947, rend_intergenic: 97391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102441, rend_intergenic: 100919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108825, rend_intergenic: 104937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119467, rend_intergenic: 109141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123147, rend_intergenic: 121420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145828, rend_intergenic: 143827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149797, rend_intergenic: 146093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158249, rend_intergenic: 151420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support
	-no exons in range 1 - 11846

-building DP trellis

-building trellis in range 153878 - 166494
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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