-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_3641058-3864869

-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_23-snap.751-T1
Valid prediction for snap_scaffold_23-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_50866-T1
Valid prediction for Augustus_model.g33988.t1
Valid prediction for snap_scaffold_23-snap.731-T1
Valid prediction for HiQ_model.g33980.t1
Valid prediction for GlimmerHMM_glimmerT_50857-T1
Valid prediction for GlimmerHMM_glimmerT_50865-T1
Valid prediction for GlimmerHMM_glimmerT_50852-T1
Valid prediction for GlimmerHMM_glimmerT_50862-T1
Valid prediction for snap_scaffold_23-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_50860-T1
Valid prediction for snap_scaffold_23-snap.754-T1
Valid prediction for snap_scaffold_23-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_50847-T1
Valid prediction for GlimmerHMM_glimmerT_50864-T1
Valid prediction for Augustus_model.g33989.t1
Valid prediction for GlimmerHMM_glimmerT_50848-T1
Valid prediction for snap_scaffold_23-snap.733-T1
Valid prediction for Augustus_model.g33990.t1
Couldn't classify 5348, 5359
Couldn't classify 9591, 10238
Sorry, prediction pasa_asmbl_31460.p1 fails validation.
(GAC)	 AG	5348-5359	GT	AGG
(GAA)	 AG	5814-5900	GT	AGG
(GAA)	 AG	6138-6174	GT	AAG
(AAC)	 AG	7822-7867	GT	TGG
(TAC)	 AG	9312-9456	GT	AGG
(GCT)	 AG	9591-10238	AC	CGA
-recovered pasa_asmbl_31460.p1, internal, 5348, 5359
-recovered pasa_asmbl_31460.p1, internal, 5814, 5900
-recovered pasa_asmbl_31460.p1, internal, 6138, 6174
-recovered pasa_asmbl_31460.p1, internal, 7822, 7867
-recovered pasa_asmbl_31460.p1, internal, 9312, 9456
Couldn't classify 10326, 10586
Couldn't classify 15517, 15601
Sorry, prediction pasa_asmbl_31462.p1 fails validation.
(GCG)	 GC	10326-10586	GT	CGG
(GCT)	 AG	10695-10810	GT	CTG
(AGC)	 AG	11913-12126	GT	AGG
(AAG)	 AG	12374-12450	GT	AGG
(ACA)	 AG	12622-12685	GT	CGG
(TCC)	 AG	14607-14743	GT	AGG
(ATT)	 AG	14865-14936	GT	TGG
(TAT)	 AG	15098-15191	GT	AGG
(AGC)	 AG	15283-15326	GT	AAG
(AGG)	 AG	15517-15601	GG	GCG
-recovered pasa_asmbl_31462.p1, internal, 10695, 10810
-recovered pasa_asmbl_31462.p1, internal, 11913, 12126
-recovered pasa_asmbl_31462.p1, internal, 12374, 12450
-recovered pasa_asmbl_31462.p1, internal, 12622, 12685
-recovered pasa_asmbl_31462.p1, internal, 14607, 14743
-recovered pasa_asmbl_31462.p1, internal, 14865, 14936
-recovered pasa_asmbl_31462.p1, internal, 15098, 15191
-recovered pasa_asmbl_31462.p1, internal, 15283, 15326
Valid prediction for snap_scaffold_23-snap.737-T1
Valid prediction for GlimmerHMM_glimmerT_50861-T1
Valid prediction for snap_scaffold_23-snap.750-T1
Valid prediction for snap_scaffold_23-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_50855-T1
Valid prediction for snap_scaffold_23-snap.732-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_23-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_50867-T1
Valid prediction for CodingQuarry_transcript_35616-T1
Valid prediction for Augustus_model.g33986.t1
Valid prediction for GlimmerHMM_glimmerT_50859-T1
Valid prediction for GlimmerHMM_glimmerT_50856-T1
Valid prediction for Augustus_model.g33984.t1
Valid prediction for snap_scaffold_23-snap.743-T1
Couldn't classify 143860, 144008
Sorry, prediction pasa_asmbl_30818.p1 fails validation.
(AAA)	 CC	143860-144008	GT	AAG
(CGA)	 AG	146596-146776	GT	AAG
-recovered pasa_asmbl_30818.p1, terminal, 146596, 146776
-recovered pasa_asmbl_30818.p1, internal, 146596, 146776
Valid prediction for GlimmerHMM_glimmerT_50846-T1
Valid prediction for snap_scaffold_23-snap.741-T1
Valid prediction for snap_scaffold_23-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_50858-T1
Couldn't classify 182917, 182977
Couldn't classify 184541, 184597
Sorry, prediction pasa_asmbl_30816.p1 fails validation.
(TGG)	 GC	182917-182977	GT	AGG
(GTA)	 AG	183531-183642	GT	AGG
(GAG)	 AG	183938-184106	GT	GGG
(AGC)	 AG	184541-184597	CG	AGC
-recovered pasa_asmbl_30816.p1, internal, 183531, 183642
-recovered pasa_asmbl_30816.p1, internal, 183938, 184106
Valid prediction for snap_scaffold_23-snap.734-T1
Valid prediction for Augustus_model.g33979.t1
Valid prediction for snap_scaffold_23-snap.742-T1
Valid prediction for Augustus_model.g33985.t1
Valid prediction for snap_scaffold_23-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_50851-T1
Valid prediction for Augustus_model.g33982.t1
Valid prediction for snap_scaffold_23-snap.755-T1
Couldn't classify 136923, 137068
Sorry, prediction pasa_asmbl_30819.p1 fails validation.
(ATG)	 GT	133426-133708	GT	AGG
(CTC)	 AG	136677-136766	GT	AGG
(CGG)	 AG	136923-137068	AA	GGA
-recovered pasa_asmbl_30819.p1, initial, 133426, 133708
-recovered pasa_asmbl_30819.p1, internal, 136677, 136766
Valid prediction for snap_scaffold_23-snap.756-T1
Valid prediction for snap_scaffold_23-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_50853-T1
Valid prediction for snap_scaffold_23-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_50849-T1
Valid prediction for snap_scaffold_23-snap.738-T1
Valid prediction for Augustus_model.g33981.t1
Valid prediction for snap_scaffold_23-snap.746-T1
Valid prediction for snap_scaffold_23-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_50850-T1
Valid prediction for snap_scaffold_23-snap.753-T1
Valid prediction for GlimmerHMM_glimmerT_50863-T1
Valid prediction for Augustus_model.g33987.t1
Valid prediction for snap_scaffold_23-snap.739-T1
Valid prediction for Augustus_model.g33983.t1
Valid prediction for GlimmerHMM_glimmerT_50854-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15970, rend_intergenic: 11850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126396, rend_intergenic: 125794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223812
-exon list size: 286


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.9    
22.2    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.8    
44.1    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.2    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.8    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
55.9    
56.2    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.8    
78.1    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 15970, rend_intergenic: 11850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126396, rend_intergenic: 125794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support