-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_19255835-19403159

-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: +)Couldn't classify 102582, 102885
Sorry, prediction pasa_asmbl_25279.p1 fails validation.
(CAC)	 CC	102582-102885	GT	CAG
(GTT)	 AG	103442-103545	GT	CGG
(GCA)	 AG	105683-105859	GC	GAG
-recovered pasa_asmbl_25279.p1, terminal, 105683, 105859
-recovered pasa_asmbl_25279.p1, internal, 103442, 103545
-recovered pasa_asmbl_25279.p1, internal, 105683, 105859
Valid prediction for GlimmerHMM_glimmerT_5654-T1
Valid prediction for Augustus_model.g3777.t1
Couldn't classify 94689, 94928
Sorry, prediction pasa_asmbl_25276.p1 fails validation.
(GGT)	 CA	94689-94928	GT	AGG
(GTG)	 AG	95250-95865	GT	AGG
(GTA)	 AG	97677-97942	GT	AGG
(GTT)	 AG	98024-98446	GA	GAG
-recovered pasa_asmbl_25276.p1, terminal, 98024, 98446
-recovered pasa_asmbl_25276.p1, internal, 95250, 95865
-recovered pasa_asmbl_25276.p1, internal, 97677, 97942
Valid prediction for GlimmerHMM_glimmerT_5645-T1
Valid prediction for snap_scaffold_2-snap.3783-T1
Valid prediction for snap_scaffold_2-snap.3781-T1
Valid prediction for snap_scaffold_2-snap.3770-T1
Valid prediction for Augustus_model.g3778.t1
Valid prediction for snap_scaffold_2-snap.3765-T1
Valid prediction for GlimmerHMM_glimmerT_5669-T1
Valid prediction for GlimmerHMM_glimmerT_5664-T1
Valid prediction for snap_scaffold_2-snap.3767-T1
Valid prediction for GlimmerHMM_glimmerT_5663-T1
Valid prediction for GlimmerHMM_glimmerT_5668-T1
Valid prediction for Augustus_model.g3782.t1
Couldn't classify 64829, 64892
Couldn't classify 66582, 66784
Sorry, prediction pasa_asmbl_25380.p1 fails validation.
(CTC)	 AG	64829-64892	GT	TGG
(AAG)	 AG	66346-66417	GT	AGG
(GGG)	 AG	66582-66784	GT	AGG
-recovered pasa_asmbl_25380.p1, internal, 64829, 64892
-recovered pasa_asmbl_25380.p1, internal, 66346, 66417
-recovered pasa_asmbl_25380.p1, internal, 66582, 66784
Valid prediction for snap_scaffold_2-snap.3777-T1
Valid prediction for CodingQuarry_transcript_28864-T1
Valid prediction for GlimmerHMM_glimmerT_5649-T1
Couldn't classify 64304, 64473
Sorry, prediction pasa_asmbl_25271.p1 fails validation.
(ATG)	 CC	59478-59658	GT	TGG
(AGT)	 AG	59855-60000	GT	AGG
(ACC)	 AG	61658-61839	GT	AGG
(ACA)	 AG	61998-62097	GT	AGG
(GTG)	 AG	62264-62385	GT	AGG
(TGA)	 AG	63124-63230	GT	AGG
(GTG)	 AG	64304-64473	GT	GGG
-recovered pasa_asmbl_25271.p1, initial, 59478, 59658
-recovered pasa_asmbl_25271.p1, terminal, 63124, 63230
-recovered pasa_asmbl_25271.p1, internal, 59855, 60000
-recovered pasa_asmbl_25271.p1, internal, 61658, 61839
-recovered pasa_asmbl_25271.p1, internal, 61998, 62097
-recovered pasa_asmbl_25271.p1, internal, 62264, 62385
-recovered pasa_asmbl_25271.p1, internal, 63124, 63230
-recovered pasa_asmbl_25271.p1, internal, 64304, 64473
Valid prediction for snap_scaffold_2-snap.3789-T1
Valid prediction for GlimmerHMM_glimmerT_5661-T1
Valid prediction for GlimmerHMM_glimmerT_5652-T1
Valid prediction for snap_scaffold_2-snap.3773-T1
Valid prediction for Augustus_model.g3780.t1
Valid prediction for HiQ_model.g3781.t1
Valid prediction for GlimmerHMM_glimmerT_5650-T1
Couldn't classify 108673, 108709
Couldn't classify 108810, 108870
Sorry, prediction CodingQuarry_transcript_28865-T1 fails validation.
(ATG)	 TT	108486-108648	GC	AGG
(TCA)	 AG	108673-108709	AG	AGA
(AGA)	 AC	108810-108870	TT	GAT
-recovered CodingQuarry_transcript_28865-T1, initial, 108486, 108648
Valid prediction for snap_scaffold_2-snap.3790-T1
Valid prediction for snap_scaffold_2-snap.3768-T1
Valid prediction for snap_scaffold_2-snap.3786-T1
Valid prediction for Augustus_model.g3779.t1
Valid prediction for snap_scaffold_2-snap.3762-T1
Valid prediction for snap_scaffold_2-snap.3775-T1
Valid prediction for GlimmerHMM_glimmerT_5670-T1
Valid prediction for snap_scaffold_2-snap.3785-T1
Valid prediction for snap_scaffold_2-snap.3776-T1
Valid prediction for GlimmerHMM_glimmerT_5658-T1
Valid prediction for snap_scaffold_2-snap.3778-T1
Valid prediction for snap_scaffold_2-snap.3761-T1
Valid prediction for GlimmerHMM_glimmerT_5666-T1
Valid prediction for CodingQuarry_transcript_28862-T1
Valid prediction for snap_scaffold_2-snap.3792-T1
Valid prediction for GlimmerHMM_glimmerT_5659-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 CodingQuarry_transcript_28859-T1
Valid prediction for pasa_asmbl_23858.p1
Valid prediction for snap_scaffold_2-snap.3772-T1
Valid prediction for GlimmerHMM_glimmerT_5651-T1
Valid prediction for snap_scaffold_2-snap.3774-T1
Valid prediction for snap_scaffold_2-snap.3764-T1
Valid prediction for GlimmerHMM_glimmerT_5653-T1
Valid prediction for HiQ_model.g3783.t1
Couldn't classify 6194, 6343
Sorry, prediction pasa_asmbl_23869.p1 fails validation.
(ATG)	 CC	4509-4703	GT	AGG
(GTT)	 AG	6194-6343	CG	CAC
-recovered pasa_asmbl_23869.p1, initial, 4509, 4703
Valid prediction for GlimmerHMM_glimmerT_5662-T1
Valid prediction for CodingQuarry_transcript_28861-T1
Valid prediction for Augustus_model.g3785.t1
Valid prediction for snap_scaffold_2-snap.3779-T1
Valid prediction for pasa_asmbl_23865.p1
Valid prediction for CodingQuarry_transcript_28866-T1
Valid prediction for CodingQuarry_transcript_28860-T1
Valid prediction for snap_scaffold_2-snap.3784-T1
Valid prediction for GlimmerHMM_glimmerT_5671-T1
Valid prediction for snap_scaffold_2-snap.3780-T1
Valid prediction for snap_scaffold_2-snap.3788-T1
Valid prediction for GlimmerHMM_glimmerT_5646-T1
Valid prediction for Augustus_model.g3786.t1
Valid prediction for snap_scaffold_2-snap.3763-T1
Valid prediction for snap_scaffold_2-snap.3791-T1
Valid prediction for GlimmerHMM_glimmerT_5648-T1
Valid prediction for snap_scaffold_2-snap.3769-T1
Valid prediction for pasa_asmbl_23860.p1
Valid prediction for GlimmerHMM_glimmerT_5660-T1
Valid prediction for Augustus_model.g3784.t1
Valid prediction for GlimmerHMM_glimmerT_5667-T1
Valid prediction for HiQ_model.g3775.t1
Valid prediction for snap_scaffold_2-snap.3766-T1
Valid prediction for GlimmerHMM_glimmerT_5647-T1
Valid prediction for GlimmerHMM_glimmerT_5644-T1
Valid prediction for GlimmerHMM_glimmerT_5655-T1
Valid prediction for GlimmerHMM_glimmerT_5657-T1
Valid prediction for Augustus_model.g3774.t1
Valid prediction for GlimmerHMM_glimmerT_5656-T1
Valid prediction for snap_scaffold_2-snap.3771-T1
Valid prediction for HiQ_model.g3776.t1
Valid prediction for snap_scaffold_2-snap.3782-T1
Valid prediction for GlimmerHMM_glimmerT_5665-T1
Valid prediction for snap_scaffold_2-snap.3787-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29171, rend_intergenic: 25822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39853, rend_intergenic: 33647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42948, rend_intergenic: 40375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55160, rend_intergenic: 47121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69091, rend_intergenic: 59857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86811, rend_intergenic: 83442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92213, rend_intergenic: 88710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98379, rend_intergenic: 93898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105686, rend_intergenic: 104719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130971, rend_intergenic: 123187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141409, rend_intergenic: 132829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147325
-exon list size: 310


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.7    
9.0    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.2    
11.5    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.1    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
17.9    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.2    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.3    
35.6    
35.9    
36.2    
36.5    
36.9    
37.2    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
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    
52.6    
52.9    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.8    
63.1    
63.5    
63.8    
64.1    
64.4    
64.7    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.8    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.1    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
84.9    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.5    
88.8    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.0    
91.3    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 29171, rend_intergenic: 25822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39853, rend_intergenic: 33647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42948, rend_intergenic: 40375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55160, rend_intergenic: 47121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69091, rend_intergenic: 59857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86811, rend_intergenic: 83442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92213, rend_intergenic: 88710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98379, rend_intergenic: 93898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105686, rend_intergenic: 104719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130971, rend_intergenic: 123187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141409, rend_intergenic: 132829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support