-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_1-242102

-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_30912-T1
Valid prediction for pasa_asmbl_10456.p1
Valid prediction for CodingQuarry_transcript_12825-T1
Couldn't classify 1, 145
Sorry, prediction HiQ_model.g20503.t1 fails validation.
(CCT)	 CG	1-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered HiQ_model.g20503.t1, terminal, 776, 859
-recovered HiQ_model.g20503.t1, internal, 333, 583
Valid prediction for snap_scaffold_13-snap.8-T1
Valid prediction for HiQ_model.g20514.t1
Valid prediction for snap_scaffold_13-snap.12-T1
Valid prediction for GlimmerHMM_glimmerT_30920-T1
Valid prediction for Augustus_model.g20515.t1
Valid prediction for CodingQuarry_transcript_12823-T1
Valid prediction for HiQ_model.g20526.t1
Valid prediction for HiQ_model.g20504.t1
Valid prediction for pasa_asmbl_10461.p1
Valid prediction for Augustus_model.g20524.t1
Valid prediction for GlimmerHMM_glimmerT_30936-T1
Valid prediction for GlimmerHMM_glimmerT_30931-T1
Valid prediction for Augustus_model.g20522.t1
Couldn't classify 31, 145
Sorry, prediction snap_scaffold_13-snap.1-T1 fails validation.
(AAT)	 AG	31-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered snap_scaffold_13-snap.1-T1, terminal, 776, 859
-recovered snap_scaffold_13-snap.1-T1, internal, 31, 145
-recovered snap_scaffold_13-snap.1-T1, internal, 333, 583
Couldn't classify 1, 145
Sorry, prediction pasa_asmbl_10446.p1 fails validation.
(CCT)	 CG	1-145	GT	CGG
(GTG)	 AG	333-583	GT	AGG
(GCA)	 AG	776-859	TT	GAT
-recovered pasa_asmbl_10446.p1, terminal, 776, 859
-recovered pasa_asmbl_10446.p1, internal, 333, 583
Couldn't classify 86345, 86647
Sorry, prediction pasa_asmbl_10457.p1 fails validation.
(ATG)	 GA	86345-86647	AC	GAA
Valid prediction for snap_scaffold_13-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_30921-T1
Valid prediction for GlimmerHMM_glimmerT_30908-T1
add_exon() Sorry, GlimmerHMM_glimmerT_30908-T1 333-661-terminal-1 is invalid.
Valid prediction for snap_scaffold_13-snap.2-T1
Valid prediction for snap_scaffold_13-snap.29-T1
Valid prediction for snap_scaffold_13-snap.18-T1
Valid prediction for GlimmerHMM_glimmerT_30918-T1
Valid prediction for snap_scaffold_13-snap.35-T1
Valid prediction for snap_scaffold_13-snap.21-T1
Valid prediction for Augustus_model.g20523.t1
Valid prediction for pasa_asmbl_10458.p1
Valid prediction for GlimmerHMM_glimmerT_30937-T1
Valid prediction for snap_scaffold_13-snap.46-T1
Valid prediction for snap_scaffold_13-snap.27-T1
Valid prediction for snap_scaffold_13-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_30932-T1
Valid prediction for GlimmerHMM_glimmerT_30926-T1
Valid prediction for GlimmerHMM_glimmerT_30909-T1
Valid prediction for snap_scaffold_13-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_30929-T1
Valid prediction for GlimmerHMM_glimmerT_30933-T1
Couldn't classify 3619, 3688
Couldn't classify 4290, 4350
Sorry, prediction CodingQuarry_transcript_12822-T1 fails validation.
(ATG)	 TC	2881-2970	GT	GAG
(AAT)	 AG	3173-3247	GT	AGG
(GTG)	 AG	3338-3434	GT	AGG
(AGC)	 AG	3619-3688	AT	AGA
(ATT)	 AC	4290-4350	GT	AAG
(CCT)	 AG	4449-4529	GT	AGG
(AAT)	 AG	4698-4784	AT	AGA
-recovered CodingQuarry_transcript_12822-T1, initial, 2881, 2970
-recovered CodingQuarry_transcript_12822-T1, terminal, 4698, 4784
-recovered CodingQuarry_transcript_12822-T1, internal, 3173, 3247
-recovered CodingQuarry_transcript_12822-T1, internal, 3338, 3434
-recovered CodingQuarry_transcript_12822-T1, internal, 4449, 4529
Valid prediction for CodingQuarry_transcript_12824-T1
Valid prediction for snap_scaffold_13-snap.42-T1
Couldn't classify 3619, 3688
Couldn't classify 4290, 4350
Sorry, prediction pasa_asmbl_10450.p1 fails validation.
(ATG)	 AA	1661-1697	GT	AGG
(GTA)	 AG	2080-2168	GT	AGG
(GGA)	 AG	2294-2361	GT	AGG
(ATT)	 AG	2514-2574	GT	AGG
(GAC)	 AG	2685-2741	GT	AGG
(TCA)	 AG	2875-2970	GT	GAG
(AAT)	 AG	3173-3247	GT	AGG
(GTG)	 AG	3338-3434	GT	AGG
(AGC)	 AG	3619-3688	AT	AGA
(ATT)	 AC	4290-4350	GT	AAG
(CCT)	 AG	4449-4529	GT	AGG
(AAT)	 AG	4698-4784	AT	AGA
-recovered pasa_asmbl_10450.p1, initial, 1661, 1697
-recovered pasa_asmbl_10450.p1, terminal, 4698, 4784
-recovered pasa_asmbl_10450.p1, internal, 2080, 2168
-recovered pasa_asmbl_10450.p1, internal, 2294, 2361
-recovered pasa_asmbl_10450.p1, internal, 2514, 2574
-recovered pasa_asmbl_10450.p1, internal, 2685, 2741
-recovered pasa_asmbl_10450.p1, internal, 2875, 2970
-recovered pasa_asmbl_10450.p1, internal, 3173, 3247
-recovered pasa_asmbl_10450.p1, internal, 3338, 3434
-recovered pasa_asmbl_10450.p1, internal, 4449, 4529
Valid prediction for snap_scaffold_13-snap.22-T1
Valid prediction for Augustus_model.g20513.t1
Valid prediction for GlimmerHMM_glimmerT_30919-T1
Valid prediction for snap_scaffold_13-snap.17-T1
Valid prediction for snap_scaffold_13-snap.20-T1
Valid prediction for Augustus_model.g20508.t1
Valid prediction for snap_scaffold_13-snap.38-T1
Valid prediction for snap_scaffold_13-snap.19-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_30917-T1
Valid prediction for GlimmerHMM_glimmerT_30915-T1
Valid prediction for snap_scaffold_13-snap.15-T1
Valid prediction for GlimmerHMM_glimmerT_30913-T1
Valid prediction for Augustus_model.g20517.t1
Valid prediction for snap_scaffold_13-snap.23-T1
Valid prediction for snap_scaffold_13-snap.7-T1
Valid prediction for Augustus_model.g20516.t1
Valid prediction for snap_scaffold_13-snap.13-T1
Valid prediction for Augustus_model.g20506.t1
Valid prediction for GlimmerHMM_glimmerT_30914-T1
Valid prediction for Augustus_model.g20507.t1
Valid prediction for snap_scaffold_13-snap.3-T1
Valid prediction for Augustus_model.g20519.t1
Valid prediction for GlimmerHMM_glimmerT_30922-T1
Valid prediction for snap_scaffold_13-snap.28-T1
Valid prediction for snap_scaffold_13-snap.44-T1
Valid prediction for Augustus_model.g20521.t1
Valid prediction for GlimmerHMM_glimmerT_30924-T1
Valid prediction for GlimmerHMM_glimmerT_30927-T1
Valid prediction for snap_scaffold_13-snap.40-T1
Valid prediction for snap_scaffold_13-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_30930-T1
Valid prediction for Augustus_model.g20510.t1
Valid prediction for GlimmerHMM_glimmerT_30923-T1
Valid prediction for snap_scaffold_13-snap.26-T1
Valid prediction for snap_scaffold_13-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_30935-T1
Valid prediction for snap_scaffold_13-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_30928-T1
Valid prediction for GlimmerHMM_glimmerT_30910-T1
Valid prediction for Augustus_model.g20509.t1
Valid prediction for snap_scaffold_13-snap.14-T1
Valid prediction for snap_scaffold_13-snap.36-T1
Valid prediction for Augustus_model.g20525.t1
Valid prediction for Augustus_model.g20505.t1
Valid prediction for snap_scaffold_13-snap.41-T1
Valid prediction for snap_scaffold_13-snap.34-T1
Valid prediction for snap_scaffold_13-snap.39-T1
Valid prediction for snap_scaffold_13-snap.24-T1
Valid prediction for snap_scaffold_13-snap.32-T1
Valid prediction for snap_scaffold_13-snap.48-T1
Valid prediction for GlimmerHMM_glimmerT_30911-T1
Valid prediction for Augustus_model.g20518.t1
Valid prediction for Augustus_model.g20512.t1
Valid prediction for snap_scaffold_13-snap.25-T1
Valid prediction for snap_scaffold_13-snap.11-T1
Valid prediction for Augustus_model.g20520.t1
Valid prediction for snap_scaffold_13-snap.33-T1
Valid prediction for snap_scaffold_13-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_30916-T1
Valid prediction for Augustus_model.g20511.t1
Valid prediction for snap_scaffold_13-snap.4-T1
Valid prediction for snap_scaffold_13-snap.5-T1
Valid prediction for snap_scaffold_13-snap.6-T1
Valid prediction for snap_scaffold_13-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_30934-T1
Valid prediction for snap_scaffold_13-snap.45-T1
Valid prediction for GlimmerHMM_glimmerT_30925-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 153678, rend_intergenic: 153675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108979, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123542, rend_intergenic: 121240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132062, rend_intergenic: 130547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242102
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
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    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 44 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 153678, rend_intergenic: 153675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108979, rend_intergenic: 102690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123542, rend_intergenic: 121240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132062, rend_intergenic: 130547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support