-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_17589330-17743664

-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_8228-T1
Valid prediction for Augustus_model.g5427.t1
Valid prediction for Augustus_model.g5418.t1
Valid prediction for snap_scaffold_3-snap.3428-T1
Valid prediction for GlimmerHMM_glimmerT_8222-T1
Valid prediction for snap_scaffold_3-snap.3426-T1
Valid prediction for snap_scaffold_3-snap.3443-T1
Valid prediction for snap_scaffold_3-snap.3445-T1
Valid prediction for CodingQuarry_transcript_46453-T1
Valid prediction for snap_scaffold_3-snap.3430-T1
Valid prediction for snap_scaffold_3-snap.3441-T1
Couldn't classify 104059, 104089
Couldn't classify 106398, 106472
Sorry, prediction CodingQuarry_transcript_46454-T1 fails validation.
(ATG)	 AA	103909-103950	GT	CTG
(GAG)	 AG	104059-104089	TG	GAT
(CCA)	 CT	106398-106472	GT	TGG
(CCT)	 AG	106856-107098	GT	AGG
(ATC)	 AG	107425-107573	AA	AGA
-recovered CodingQuarry_transcript_46454-T1, initial, 103909, 103950
-recovered CodingQuarry_transcript_46454-T1, terminal, 107425, 107573
-recovered CodingQuarry_transcript_46454-T1, internal, 106856, 107098
Valid prediction for pasa_asmbl_40689.p1
Valid prediction for GlimmerHMM_glimmerT_8226-T1
Valid prediction for snap_scaffold_3-snap.3442-T1
Valid prediction for Augustus_model.g5417.t1
Valid prediction for Augustus_model.g5426.t1
Valid prediction for CodingQuarry_transcript_46452-T1
Valid prediction for snap_scaffold_3-snap.3432-T1
Valid prediction for snap_scaffold_3-snap.3434-T1
Valid prediction for HiQ_model.g5424.t1
Valid prediction for snap_scaffold_3-snap.3436-T1
Valid prediction for GlimmerHMM_glimmerT_8233-T1
Valid prediction for snap_scaffold_3-snap.3440-T1
Valid prediction for snap_scaffold_3-snap.3447-T1
Valid prediction for snap_scaffold_3-snap.3444-T1
Valid prediction for GlimmerHMM_glimmerT_8236-T1
Valid prediction for GlimmerHMM_glimmerT_8225-T1
Valid prediction for GlimmerHMM_glimmerT_8234-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 Augustus_model.g5423.t1
Valid prediction for GlimmerHMM_glimmerT_8235-T1
Valid prediction for Augustus_model.g5428.t1
Valid prediction for GlimmerHMM_glimmerT_8230-T1
Valid prediction for snap_scaffold_3-snap.3429-T1
Valid prediction for snap_scaffold_3-snap.3446-T1
Valid prediction for GlimmerHMM_glimmerT_8237-T1
Valid prediction for snap_scaffold_3-snap.3435-T1
Valid prediction for Augustus_model.g5422.t1
Valid prediction for Augustus_model.g5419.t1
Valid prediction for Augustus_model.g5425.t1
Valid prediction for GlimmerHMM_glimmerT_8224-T1
Valid prediction for GlimmerHMM_glimmerT_8223-T1
Valid prediction for GlimmerHMM_glimmerT_8232-T1
Valid prediction for GlimmerHMM_glimmerT_8231-T1
Valid prediction for snap_scaffold_3-snap.3425-T1
Valid prediction for snap_scaffold_3-snap.3431-T1
Valid prediction for HiQ_model.g5420.t1
Valid prediction for GlimmerHMM_glimmerT_8227-T1
Valid prediction for GlimmerHMM_glimmerT_8229-T1
Valid prediction for GlimmerHMM_glimmerT_8240-T1
Valid prediction for GlimmerHMM_glimmerT_8221-T1
Valid prediction for GlimmerHMM_glimmerT_8239-T1
Valid prediction for pasa_asmbl_39574.p1
Valid prediction for snap_scaffold_3-snap.3427-T1
Valid prediction for GlimmerHMM_glimmerT_8238-T1
Valid prediction for snap_scaffold_3-snap.3433-T1
Valid prediction for snap_scaffold_3-snap.3438-T1
Valid prediction for snap_scaffold_3-snap.3437-T1
Valid prediction for snap_scaffold_3-snap.3439-T1
Valid prediction for HiQ_model.g5421.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8713, rend_intergenic: 8536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13806, rend_intergenic: 9869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21964, rend_intergenic: 19135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33658, rend_intergenic: 29958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154335
-exon list size: 158


building trellis

0.6    
1.2    
1.9    
2.5    
3.1    
3.8    
4.4    
5.0    
5.6    
6.2    
6.9    
7.5    
8.1    
8.8    
9.4    
10.0    
10.6    
11.2    
11.9    
12.5    
13.1    
13.8    
14.4    
15.0    
15.6    
16.2    
16.9    
17.5    
18.1    
18.8    
19.4    
20.0    
20.6    
21.2    
21.9    
22.5    
23.1    
23.8    
24.4    
25.0    
25.6    
26.2    
26.9    
27.5    
28.1    
28.7    
29.4    
30.0    
30.6    
31.2    
31.9    
32.5    
33.1    
33.8    
34.4    
35.0    
35.6    
36.2    
36.9    
37.5    
38.1    
38.8    
39.4    
40.0    
40.6    
41.2    
41.9    
42.5    
43.1    
43.8    
44.4    
45.0    
45.6    
46.2    
46.9    
47.5    
48.1    
48.8    
49.4    
50.0    
50.6    
51.2    
51.9    
52.5    
53.1    
53.8    
54.4    
55.0    
55.6    
56.2    
56.9    
57.5    
58.1    
58.8    
59.4    
60.0    
60.6    
61.3    
61.9    
62.5    
63.1    
63.7    
64.4    
65.0    
65.6    
66.2    
66.9    
67.5    
68.1    
68.8    
69.4    
70.0    
70.6    
71.2    
71.9    
72.5    
73.1    
73.8    
74.4    
75.0    
75.6    
76.2    
76.9    
77.5    
78.1    
78.8    
79.4    
80.0    
80.6    
81.2    
81.9    
82.5    
83.1    
83.8    
84.4    
85.0    
85.6    
86.2    
86.9    
87.5    
88.1    
88.8    
89.4    
90.0    
90.6    
91.2    
91.9    
92.5    
93.1    
93.8    
94.4    
95.0    
95.6    
96.2    
96.9    
97.5    
98.1    
98.8    
99.4    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 8713, rend_intergenic: 8536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13806, rend_intergenic: 9869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21964, rend_intergenic: 19135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33658, rend_intergenic: 29958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 141494 - 154335
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support