-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_3978632-4207913

-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.g26726.t1
Valid prediction for Augustus_model.g26731.t1
Couldn't classify 227443, 227544
Sorry, prediction CodingQuarry_transcript_21943-T1 fails validation.
(ATG)	 CC	226595-226699	GC	TGG
(GAC)	 TA	227443-227544	GT	GGG
(GTG)	 AG	227649-227702	AA	AAA
-recovered CodingQuarry_transcript_21943-T1, initial, 226595, 226699
-recovered CodingQuarry_transcript_21943-T1, terminal, 227649, 227702
Valid prediction for GlimmerHMM_glimmerT_40120-T1
Couldn't classify 92332, 95421
Sorry, prediction pasa_asmbl_18767.p1 fails validation.
(GCT)	 TA	92332-95421	TT	GAT
Valid prediction for snap_scaffold_17-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_40132-T1
Valid prediction for GlimmerHMM_glimmerT_40130-T1
Valid prediction for snap_scaffold_17-snap.870-T1
Valid prediction for CodingQuarry_transcript_21938-T1
Valid prediction for snap_scaffold_17-snap.839-T1
Valid prediction for snap_scaffold_17-snap.862-T1
Valid prediction for snap_scaffold_17-snap.844-T1
Valid prediction for Augustus_model.g26720.t1
Valid prediction for GlimmerHMM_glimmerT_40143-T1
Valid prediction for snap_scaffold_17-snap.865-T1
Valid prediction for snap_scaffold_17-snap.873-T1
Valid prediction for pasa_asmbl_18763.p1
Valid prediction for GlimmerHMM_glimmerT_40116-T1
Valid prediction for GlimmerHMM_glimmerT_40142-T1
Valid prediction for snap_scaffold_17-snap.852-T1
Valid prediction for CodingQuarry_transcript_21940-T1
Valid prediction for GlimmerHMM_glimmerT_40117-T1
Valid prediction for GlimmerHMM_glimmerT_40126-T1
Valid prediction for Augustus_model.g26734.t1
Valid prediction for GlimmerHMM_glimmerT_40129-T1
Valid prediction for Augustus_model.g26733.t1
Valid prediction for GlimmerHMM_glimmerT_40123-T1
Couldn't classify 226908, 226964
Sorry, prediction CodingQuarry_transcript_21944-T1 fails validation.
(ATG)	 CC	226595-226699	GC	TGG
(GAG)	 TA	226908-226964	CG	AAC
-recovered CodingQuarry_transcript_21944-T1, initial, 226595, 226699
Couldn't classify 91300, 91635
Sorry, prediction pasa_asmbl_18766.p1 fails validation.
(ATG)	 AG	91300-91635	GG	GCG
Valid prediction for GlimmerHMM_glimmerT_40124-T1
Valid prediction for GlimmerHMM_glimmerT_40135-T1
Valid prediction for snap_scaffold_17-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_40139-T1
Valid prediction for snap_scaffold_17-snap.855-T1
Couldn't classify 106990, 107181
Sorry, prediction pasa_asmbl_18769.p2 fails validation.
(CCT)	 CC	106990-107181	GT	AGG
(GAT)	 AG	107635-107850	GG	GAG
-recovered pasa_asmbl_18769.p2, terminal, 107635, 107850
Valid prediction for Augustus_model.g26727.t1
Valid prediction for GlimmerHMM_glimmerT_40137-T1
Valid prediction for Augustus_model.g26736.t1
Valid prediction for Augustus_model.g26724.t1
Valid prediction for GlimmerHMM_glimmerT_40136-T1
Couldn't classify 67924, 68107
Sorry, prediction pasa_asmbl_18765.p1 fails validation.
(CTG)	 CC	67924-68107	GT	TAG
(GTT)	 AG	68245-68350	GT	CCG
(GAA)	 AG	68517-68658	GT	AGG
(CCT)	 AG	68770-68866	GT	TGG
(ACA)	 AG	69028-69226	GT	AGG
(GCA)	 AG	69347-69479	GT	AGG
(GGT)	 AG	69611-69736	GT	AGG
(GGC)	 AG	69918-70016	TG	GAT
-recovered pasa_asmbl_18765.p1, terminal, 69918, 70016
-recovered pasa_asmbl_18765.p1, internal, 68245, 68350
-recovered pasa_asmbl_18765.p1, internal, 68517, 68658
-recovered pasa_asmbl_18765.p1, internal, 68770, 68866
-recovered pasa_asmbl_18765.p1, internal, 69028, 69226
-recovered pasa_asmbl_18765.p1, internal, 69347, 69479
-recovered pasa_asmbl_18765.p1, internal, 69611, 69736
Valid prediction for HiQ_model.g26716.t1
Couldn't classify 64846, 64974
Couldn't classify 66232, 66377
Sorry, prediction pasa_asmbl_18764.p1 fails validation.
(CAA)	 AG	64846-64974	GT	CGG
(AAC)	 AG	65070-65165	GT	AGG
(GAT)	 AG	65825-66038	GT	CCG
(CTA)	 AG	66232-66377	CC	CCC
-recovered pasa_asmbl_18764.p1, internal, 64846, 64974
-recovered pasa_asmbl_18764.p1, internal, 65070, 65165
-recovered pasa_asmbl_18764.p1, internal, 65825, 66038
Valid prediction for HiQ_model.g26718.t1
Valid prediction for snap_scaffold_17-snap.849-T1
Valid prediction for snap_scaffold_17-snap.859-T1
Valid prediction for snap_scaffold_17-snap.875-T1
Valid prediction for snap_scaffold_17-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_40133-T1
Valid prediction for snap_scaffold_17-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_40140-T1
Couldn't classify 19027, 19456
Sorry, prediction pasa_asmbl_18758.p1 fails validation.
(GTG)	 GT	19027-19456	GT	AGG
(ACA)	 AG	19644-19966	AT	AGA
-recovered pasa_asmbl_18758.p1, terminal, 19644, 19966
Valid prediction for Augustus_model.g26729.t1
Valid prediction for Augustus_model.g26725.t1
Valid prediction for GlimmerHMM_glimmerT_40113-T1
Valid prediction for GlimmerHMM_glimmerT_40121-T1
Valid prediction for GlimmerHMM_glimmerT_40138-T1
Valid prediction for Augustus_model.g26728.t1
Valid prediction for HiQ_model.g26717.t1
Valid prediction for snap_scaffold_17-snap.840-T1
Valid prediction for snap_scaffold_17-snap.851-T1
Valid prediction for Augustus_model.g26737.t1
Valid prediction for snap_scaffold_17-snap.878-T1
Valid prediction for snap_scaffold_17-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_40115-T1
Valid prediction for CodingQuarry_transcript_21939-T1
Valid prediction for snap_scaffold_17-snap.837-T1
Valid prediction for snap_scaffold_17-snap.853-T1
Valid prediction for Augustus_model.g26721.t1
Valid prediction for snap_scaffold_17-snap.838-T1
Valid prediction for snap_scaffold_17-snap.867-T1
Valid prediction for snap_scaffold_17-snap.874-T1
Valid prediction for snap_scaffold_17-snap.854-T1
Valid prediction for GlimmerHMM_glimmerT_40128-T1
Valid prediction for GlimmerHMM_glimmerT_40144-T1
Valid prediction for snap_scaffold_17-snap.841-T1
Valid prediction for Augustus_model.g26730.t1
Valid prediction for GlimmerHMM_glimmerT_40127-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_17-snap.869-T1
Valid prediction for CodingQuarry_transcript_21942-T1
Valid prediction for snap_scaffold_17-snap.848-T1
Valid prediction for HiQ_model.g26735.t1
Valid prediction for snap_scaffold_17-snap.866-T1
Couldn't classify 19050, 19104
Sorry, prediction pasa_asmbl_17844.p1 fails validation.
(CTC)	 CC	19050-19104	GT	AGG
(ATT)	 AG	21533-21607	GT	GAG
(ATC)	 AG	21764-21901	GT	AGG
(GCA)	 AG	22618-22838	TG	AGT
-recovered pasa_asmbl_17844.p1, terminal, 22618, 22838
-recovered pasa_asmbl_17844.p1, internal, 21533, 21607
-recovered pasa_asmbl_17844.p1, internal, 21764, 21901
Valid prediction for pasa_asmbl_17837.p1
Valid prediction for pasa_asmbl_17835.p1
Valid prediction for HiQ_model.g26713.t1
Valid prediction for snap_scaffold_17-snap.864-T1
Couldn't classify 213711, 214316
Sorry, prediction pasa_asmbl_17839.p1 fails validation.
(GCA)	 CA	213711-214316	GG	GAG
Valid prediction for snap_scaffold_17-snap.877-T1
Valid prediction for HiQ_model.g26714.t1
Valid prediction for CodingQuarry_transcript_21937-T1
Valid prediction for snap_scaffold_17-snap.834-T1
Valid prediction for Augustus_model.g26732.t1
Valid prediction for snap_scaffold_17-snap.856-T1
Valid prediction for snap_scaffold_17-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_40131-T1
Valid prediction for Augustus_model.g26719.t1
Valid prediction for snap_scaffold_17-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_40114-T1
Valid prediction for snap_scaffold_17-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_40125-T1
Valid prediction for snap_scaffold_17-snap.845-T1
Valid prediction for snap_scaffold_17-snap.860-T1
Valid prediction for snap_scaffold_17-snap.836-T1
Valid prediction for snap_scaffold_17-snap.842-T1
Valid prediction for GlimmerHMM_glimmerT_40141-T1
Valid prediction for snap_scaffold_17-snap.835-T1
Valid prediction for GlimmerHMM_glimmerT_40122-T1
Valid prediction for Augustus_model.g26715.t1
Valid prediction for snap_scaffold_17-snap.857-T1
Couldn't classify 211450, 211497
Couldn't classify 213240, 213551
Sorry, prediction pasa_asmbl_18459.p1 fails validation.
(TGG)	 AA	211450-211497	GT	AGG
(AAA)	 AG	213240-213551	TT	AGT
Valid prediction for GlimmerHMM_glimmerT_40118-T1
Valid prediction for CodingQuarry_transcript_21936-T1
Valid prediction for snap_scaffold_17-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_40112-T1
Valid prediction for snap_scaffold_17-snap.863-T1
Valid prediction for snap_scaffold_17-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_40119-T1
Valid prediction for Augustus_model.g26723.t1
Valid prediction for GlimmerHMM_glimmerT_40134-T1
Valid prediction for snap_scaffold_17-snap.846-T1
Valid prediction for Augustus_model.g26722.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 46353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120240, rend_intergenic: 118212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159138, rend_intergenic: 143922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174473, rend_intergenic: 171214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185198, rend_intergenic: 178902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188435, rend_intergenic: 186236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191582, rend_intergenic: 189849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200149, rend_intergenic: 198084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229282
-exon list size: 371


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 46812, rend_intergenic: 46353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120240, rend_intergenic: 118212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159138, rend_intergenic: 143922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174473, rend_intergenic: 171214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185198, rend_intergenic: 178902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188435, rend_intergenic: 186236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191582, rend_intergenic: 189849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200149, rend_intergenic: 198084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support