-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_6298301-6375867

-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_6638-T1
Valid prediction for snap_scaffold_3-snap.1296-T1
Valid prediction for Augustus_model.g4314.t1
Valid prediction for Augustus_model.g4319.t1
Valid prediction for snap_scaffold_3-snap.1292-T1
Valid prediction for snap_scaffold_3-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_6642-T1
Valid prediction for snap_scaffold_3-snap.1295-T1
Valid prediction for snap_scaffold_3-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_6647-T1
Valid prediction for Augustus_model.g4315.t1
Valid prediction for GlimmerHMM_glimmerT_6639-T1
Valid prediction for GlimmerHMM_glimmerT_6651-T1
Valid prediction for GlimmerHMM_glimmerT_6645-T1
Valid prediction for GlimmerHMM_glimmerT_6644-T1
Valid prediction for snap_scaffold_3-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_6641-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_3-snap.1294-T1
Valid prediction for snap_scaffold_3-snap.1291-T1
Couldn't classify 73014, 73060
Sorry, prediction pasa_asmbl_38947.p1 fails validation.
(ATG)	 AA	69493-69625	GT	AGG
(ATG)	 AG	69875-70000	GT	GGG
(CTG)	 AG	70257-70394	GT	AAG
(ACC)	 AG	70547-70678	GT	CGG
(CGG)	 AG	70801-70938	GT	AAG
(ACC)	 AG	71722-71880	GT	GGG
(GCA)	 AG	72104-72301	GT	GGG
(AGG)	 AG	72428-72610	GT	CGG
(TCA)	 AG	73014-73060	TT	AGT
-recovered pasa_asmbl_38947.p1, initial, 69493, 69625
add_exon() Sorry, pasa_asmbl_38947.p1 69875-70000-initial-1 is invalid.
-recovered pasa_asmbl_38947.p1, initial, 69875, 70000
-recovered pasa_asmbl_38947.p1, internal, 69875, 70000
-recovered pasa_asmbl_38947.p1, internal, 70257, 70394
-recovered pasa_asmbl_38947.p1, internal, 70547, 70678
-recovered pasa_asmbl_38947.p1, internal, 70801, 70938
-recovered pasa_asmbl_38947.p1, internal, 71722, 71880
-recovered pasa_asmbl_38947.p1, internal, 72104, 72301
-recovered pasa_asmbl_38947.p1, internal, 72428, 72610
Valid prediction for snap_scaffold_3-snap.1297-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g4313.t1
Valid prediction for GlimmerHMM_glimmerT_6646-T1
Valid prediction for GlimmerHMM_glimmerT_6650-T1
Valid prediction for GlimmerHMM_glimmerT_6649-T1
Valid prediction for GlimmerHMM_glimmerT_6648-T1
Valid prediction for GlimmerHMM_glimmerT_6643-T1
Valid prediction for snap_scaffold_3-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_6640-T1
Couldn't classify 74993, 75122
Couldn't classify 77125, 77258
Sorry, prediction pasa_asmbl_39783.p1 fails validation.
(GAC)	 TA	74993-75122	GT	TGG
(ATC)	 AG	75219-75362	GT	AGG
(GTG)	 AG	77125-77258	AG	GCA
-recovered pasa_asmbl_39783.p1, internal, 75219, 75362
Valid prediction for snap_scaffold_3-snap.1286-T1
Valid prediction for snap_scaffold_3-snap.1284-T1
Valid prediction for Augustus_model.g4318.t1
Valid prediction for snap_scaffold_3-snap.1288-T1
Valid prediction for Augustus_model.g4317.t1
Valid prediction for Augustus_model.g4316.t1
Valid prediction for snap_scaffold_3-snap.1285-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23668, rend_intergenic: 12538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34709, rend_intergenic: 33512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40653, rend_intergenic: 35098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51288, rend_intergenic: 40725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65500, rend_intergenic: 61242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71121, rend_intergenic: 69459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 77567
-exon list size: 145


building trellis

0.7    
1.4    
2.0    
2.7    
3.4    
4.1    
4.8    
5.4    
6.1    
6.8    
7.5    
8.2    
8.8    
9.5    
10.2    
10.9    
11.6    
12.2    
12.9    
13.6    
14.3    
15.0    
15.6    
16.3    
17.0    
17.7    
18.4    
19.0    
19.7    
20.4    
21.1    
21.8    
22.4    
23.1    
23.8    
24.5    
25.2    
25.9    
26.5    
27.2    
27.9    
28.6    
29.3    
29.9    
30.6    
31.3    
32.0    
32.7    
33.3    
34.0    
34.7    
35.4    
36.1    
36.7    
37.4    
38.1    
38.8    
39.5    
40.1    
40.8    
41.5    
42.2    
42.9    
43.5    
44.2    
44.9    
45.6    
46.3    
46.9    
47.6    
48.3    
49.0    
49.7    
50.3    
51.0    
51.7    
52.4    
53.1    
53.7    
54.4    
55.1    
55.8    
56.5    
57.1    
57.8    
58.5    
59.2    
59.9    
60.5    
61.2    
61.9    
62.6    
63.3    
63.9    
64.6    
65.3    
66.0    
66.7    
67.3    
68.0    
68.7    
69.4    
70.1    
70.7    
71.4    
72.1    
72.8    
73.5    
74.1    
74.8    
75.5    
76.2    
76.9    
77.6    
78.2    
78.9    
79.6    
80.3    
81.0    
81.6    
82.3    
83.0    
83.7    
84.4    
85.0    
85.7    
86.4    
87.1    
87.8    
88.4    
89.1    
89.8    
90.5    
91.2    
91.8    
92.5    
93.2    
93.9    
94.6    
95.2    
95.9    
96.6    
97.3    
98.0    
98.6    
99.3    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 23668, rend_intergenic: 12538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34709, rend_intergenic: 33512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40653, rend_intergenic: 35098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51288, rend_intergenic: 40725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65500, rend_intergenic: 61242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71121, rend_intergenic: 69459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support