-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1751535-1941748

-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 Augustus_model.g3975.t1
Valid prediction for GlimmerHMM_glimmerT_6083-T1
Valid prediction for GlimmerHMM_glimmerT_6079-T1
Valid prediction for Augustus_model.g3968.t1
Valid prediction for snap_scaffold_3-snap.455-T1
Valid prediction for GlimmerHMM_glimmerT_6088-T1
Valid prediction for snap_scaffold_3-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_6081-T1
Valid prediction for snap_scaffold_3-snap.449-T1
Valid prediction for snap_scaffold_3-snap.448-T1
Valid prediction for GlimmerHMM_glimmerT_6078-T1
Valid prediction for Augustus_model.g3976.t1
Valid prediction for CodingQuarry_transcript_46094-T1
Valid prediction for snap_scaffold_3-snap.438-T1
Valid prediction for snap_scaffold_3-snap.436-T1
Valid prediction for Augustus_model.g3966.t1
Valid prediction for CodingQuarry_transcript_46093-T1
Valid prediction for pasa_asmbl_39880.p1
Valid prediction for Augustus_model.g3973.t1
Valid prediction for GlimmerHMM_glimmerT_6090-T1
Valid prediction for snap_scaffold_3-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_6094-T1
Valid prediction for snap_scaffold_3-snap.429-T1
Valid prediction for pasa_asmbl_39892.p1
Couldn't classify 24935, 25276
Sorry, prediction pasa_asmbl_39884.p1 fails validation.
(GGA)	 AA	24935-25276	GT	AGG
(GCC)	 AG	25557-25628	GT	ATG
(CTG)	 AG	25738-25864	GT	TGG
(GGC)	 AG	26017-26164	GT	GAG
(GTT)	 AG	26364-26442	CA	AAC
-recovered pasa_asmbl_39884.p1, terminal, 26364, 26442
-recovered pasa_asmbl_39884.p1, internal, 25557, 25628
-recovered pasa_asmbl_39884.p1, internal, 25738, 25864
-recovered pasa_asmbl_39884.p1, internal, 26017, 26164
Valid prediction for GlimmerHMM_glimmerT_6084-T1
Valid prediction for Augustus_model.g3977.t1
Valid prediction for GlimmerHMM_glimmerT_6098-T1
Valid prediction for Augustus_model.g3969.t1
Valid prediction for snap_scaffold_3-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_6095-T1
Valid prediction for GlimmerHMM_glimmerT_6082-T1
Valid prediction for GlimmerHMM_glimmerT_6080-T1
Valid prediction for snap_scaffold_3-snap.454-T1
Valid prediction for snap_scaffold_3-snap.428-T1
Valid prediction for HiQ_model.g3972.t1
Valid prediction for CodingQuarry_transcript_46090-T1
Valid prediction for Augustus_model.g3974.t1
Valid prediction for HiQ_model.g3964.t1
Valid prediction for snap_scaffold_3-snap.456-T1
Valid prediction for snap_scaffold_3-snap.452-T1
Valid prediction for snap_scaffold_3-snap.441-T1
Valid prediction for GlimmerHMM_glimmerT_6077-T1
Valid prediction for CodingQuarry_transcript_46095-T1
Couldn't classify 78867, 79086
Sorry, prediction pasa_asmbl_39888.p1 fails validation.
(ATG)	 AA	73512-73633	GT	AGG
(GGG)	 AG	74608-74820	GT	TAG
(CGC)	 AG	75772-75910	GT	AGG
(CCT)	 AG	77826-77952	GT	GGG
(CAC)	 AG	78093-78141	GT	TGG
(GAG)	 AG	78277-78456	GT	GAG
(AGA)	 AG	78867-79086	GG	CCG
-recovered pasa_asmbl_39888.p1, initial, 73512, 73633
-recovered pasa_asmbl_39888.p1, internal, 74608, 74820
-recovered pasa_asmbl_39888.p1, internal, 75772, 75910
-recovered pasa_asmbl_39888.p1, internal, 77826, 77952
-recovered pasa_asmbl_39888.p1, internal, 78093, 78141
-recovered pasa_asmbl_39888.p1, internal, 78277, 78456
Valid prediction for GlimmerHMM_glimmerT_6085-T1
Valid prediction for snap_scaffold_3-snap.432-T1
Valid prediction for snap_scaffold_3-snap.451-T1
Couldn't classify 1996, 2013
Couldn't classify 13005, 13175
Sorry, prediction pasa_asmbl_39873.p1 fails validation.
(ATC)	 AG	1996-2013	GT	AGG
(AAA)	 AG	2286-2357	GT	TGG
(GAG)	 AG	3962-4006	GT	CGG
(ATC)	 AG	4653-4703	GT	GGG
(TCA)	 AG	5175-5210	GT	GGG
(GGT)	 AG	6343-6408	GT	ACG
(AGC)	 AG	6507-6548	GT	GGG
(AGC)	 AG	7441-7500	GT	CGG
(GCA)	 AG	7922-8005	GT	AGG
(GCC)	 AG	9139-9201	GT	GCG
(CCC)	 AG	9924-9995	GT	TGG
(GAT)	 AG	10445-10543	GT	ACG
(AGC)	 AG	11546-11572	GT	AGG
(GGT)	 AG	11677-11802	GT	AAG
(GAG)	 AG	12289-12360	GT	AGG
(GAC)	 AG	13005-13175	GT	AGG
-recovered pasa_asmbl_39873.p1, internal, 1996, 2013
-recovered pasa_asmbl_39873.p1, internal, 2286, 2357
-recovered pasa_asmbl_39873.p1, internal, 3962, 4006
-recovered pasa_asmbl_39873.p1, internal, 4653, 4703
-recovered pasa_asmbl_39873.p1, internal, 5175, 5210
-recovered pasa_asmbl_39873.p1, internal, 6343, 6408
-recovered pasa_asmbl_39873.p1, internal, 6507, 6548
-recovered pasa_asmbl_39873.p1, internal, 7441, 7500
-recovered pasa_asmbl_39873.p1, internal, 7922, 8005
-recovered pasa_asmbl_39873.p1, internal, 9139, 9201
-recovered pasa_asmbl_39873.p1, internal, 9924, 9995
-recovered pasa_asmbl_39873.p1, internal, 10445, 10543
-recovered pasa_asmbl_39873.p1, internal, 11546, 11572
-recovered pasa_asmbl_39873.p1, internal, 11677, 11802
-recovered pasa_asmbl_39873.p1, internal, 12289, 12360
-recovered pasa_asmbl_39873.p1, internal, 13005, 13175
Valid prediction for HiQ_model.g3970.t1
Valid prediction for snap_scaffold_3-snap.461-T1
Valid prediction for CodingQuarry_transcript_46089-T1
Valid prediction for snap_scaffold_3-snap.431-T1
Valid prediction for snap_scaffold_3-snap.446-T1
Valid prediction for Augustus_model.g3967.t1
Valid prediction for GlimmerHMM_glimmerT_6091-T1
Valid prediction for snap_scaffold_3-snap.426-T1
Valid prediction for snap_scaffold_3-snap.443-T1
Valid prediction for snap_scaffold_3-snap.435-T1
Valid prediction for CodingQuarry_transcript_46091-T1
Couldn't classify 13606, 13674
Couldn't classify 15356, 15402
Sorry, prediction pasa_asmbl_39878.p1 fails validation.
(CAC)	 TG	13606-13674	GT	CCG
(GAG)	 AG	14034-14126	GT	GGG
(GCC)	 AG	14361-14453	GT	AGG
(AAA)	 AG	14778-14919	GT	GGG
(TTG)	 AG	15356-15402	AG	CGA
-recovered pasa_asmbl_39878.p1, internal, 14034, 14126
-recovered pasa_asmbl_39878.p1, internal, 14361, 14453
-recovered pasa_asmbl_39878.p1, internal, 14778, 14919

-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_3-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_6089-T1
Valid prediction for snap_scaffold_3-snap.460-T1
Valid prediction for GlimmerHMM_glimmerT_6086-T1
Valid prediction for HiQ_model.g3971.t1
Valid prediction for snap_scaffold_3-snap.442-T1
Valid prediction for snap_scaffold_3-snap.439-T1
Valid prediction for Augustus_model.g3965.t1
Valid prediction for snap_scaffold_3-snap.430-T1
Valid prediction for pasa_asmbl_38725.p1
Valid prediction for CodingQuarry_transcript_46092-T1
Valid prediction for GlimmerHMM_glimmerT_6076-T1
Valid prediction for snap_scaffold_3-snap.459-T1
Valid prediction for GlimmerHMM_glimmerT_6096-T1
Valid prediction for snap_scaffold_3-snap.447-T1
Valid prediction for snap_scaffold_3-snap.434-T1
Valid prediction for snap_scaffold_3-snap.433-T1
Valid prediction for snap_scaffold_3-snap.450-T1
Valid prediction for Augustus_model.g3978.t1
Valid prediction for snap_scaffold_3-snap.457-T1
Valid prediction for GlimmerHMM_glimmerT_6087-T1
Valid prediction for GlimmerHMM_glimmerT_6092-T1
Valid prediction for snap_scaffold_3-snap.463-T1
Couldn't classify 103636, 104025
Couldn't classify 105717, 105987
Sorry, prediction pasa_asmbl_38728.p1 fails validation.
(TTA)	 TT	103636-104025	GT	AGG
(AAC)	 AG	105233-105462	GT	AGG
(AGC)	 AG	105717-105987	CT	AGC
-recovered pasa_asmbl_38728.p1, internal, 105233, 105462
Valid prediction for Augustus_model.g3980.t1
Valid prediction for snap_scaffold_3-snap.462-T1
Valid prediction for snap_scaffold_3-snap.444-T1
Valid prediction for GlimmerHMM_glimmerT_6097-T1
Valid prediction for snap_scaffold_3-snap.437-T1
Valid prediction for Augustus_model.g3979.t1
Valid prediction for GlimmerHMM_glimmerT_6093-T1
Valid prediction for snap_scaffold_3-snap.427-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10630, rend_intergenic: 7324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34498, rend_intergenic: 28186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49079, rend_intergenic: 46848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54982, rend_intergenic: 49627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70590, rend_intergenic: 55087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79107, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112042, rend_intergenic: 110834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190214
-exon list size: 357


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.1    
3.3    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 10630, rend_intergenic: 7324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34498, rend_intergenic: 28186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49079, rend_intergenic: 46848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54982, rend_intergenic: 49627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70590, rend_intergenic: 55087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79107, rend_intergenic: 75549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112042, rend_intergenic: 110834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support