-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_8198626-8317591

-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_28-snap.1878-T1
Valid prediction for snap_scaffold_28-snap.1858-T1
Valid prediction for CodingQuarry_transcript_43736-T1
Valid prediction for snap_scaffold_28-snap.1873-T1
Valid prediction for snap_scaffold_28-snap.1861-T1
Valid prediction for snap_scaffold_28-snap.1850-T1
Valid prediction for GlimmerHMM_glimmerT_59232-T1
Valid prediction for GlimmerHMM_glimmerT_59237-T1
Valid prediction for snap_scaffold_28-snap.1869-T1
Valid prediction for Augustus_model.g39257.t1
Valid prediction for snap_scaffold_28-snap.1852-T1
Valid prediction for snap_scaffold_28-snap.1882-T1
Valid prediction for Augustus_model.g39250.t1
Valid prediction for snap_scaffold_28-snap.1864-T1
Valid prediction for Augustus_model.g39259.t1
Valid prediction for Augustus_model.g39255.t1
Valid prediction for snap_scaffold_28-snap.1854-T1
Valid prediction for snap_scaffold_28-snap.1866-T1
Valid prediction for GlimmerHMM_glimmerT_59234-T1
Valid prediction for snap_scaffold_28-snap.1863-T1
Valid prediction for snap_scaffold_28-snap.1862-T1
Couldn't classify 77382, 77432
Sorry, prediction pasa_asmbl_37736.p1 fails validation.
(ATG)	 CA	75361-75470	GT	AGG
(TGG)	 AG	75885-75998	GT	GGG
(GCT)	 AG	76310-76472	GT	AGG
(GGA)	 AG	77382-77432	GC	CTG
-recovered pasa_asmbl_37736.p1, initial, 75361, 75470
-recovered pasa_asmbl_37736.p1, internal, 75885, 75998
-recovered pasa_asmbl_37736.p1, internal, 76310, 76472
-recovered pasa_asmbl_37736.p1, internal, 77382, 77432
Valid prediction for Augustus_model.g39254.t1
Valid prediction for Augustus_model.g39260.t1
Valid prediction for GlimmerHMM_glimmerT_59242-T1
Valid prediction for snap_scaffold_28-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_59233-T1
Couldn't classify 64898, 64987
Sorry, prediction pasa_asmbl_37731.p1 fails validation.
(GGT)	 CA	64898-64987	GT	AGG
(AGT)	 AG	65087-65146	GT	GGG
(GGA)	 AG	65298-65384	GT	AGG
(CTT)	 AG	65752-65832	GT	AGG
(CTC)	 AG	65985-66210	GT	TGG
(GTG)	 AG	66383-66494	GT	AGG
(CAC)	 AG	66656-66926	GC	AGG
-recovered pasa_asmbl_37731.p1, terminal, 66656, 66926
-recovered pasa_asmbl_37731.p1, internal, 65087, 65146
-recovered pasa_asmbl_37731.p1, internal, 65298, 65384
-recovered pasa_asmbl_37731.p1, internal, 65752, 65832
-recovered pasa_asmbl_37731.p1, internal, 65985, 66210
-recovered pasa_asmbl_37731.p1, internal, 66383, 66494
-recovered pasa_asmbl_37731.p1, internal, 66656, 66926
Valid prediction for GlimmerHMM_glimmerT_59235-T1
Valid prediction for snap_scaffold_28-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_59239-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_28-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_59251-T1
Valid prediction for GlimmerHMM_glimmerT_59236-T1
Valid prediction for GlimmerHMM_glimmerT_59248-T1
Valid prediction for GlimmerHMM_glimmerT_59247-T1
Valid prediction for Augustus_model.g39253.t1
Valid prediction for GlimmerHMM_glimmerT_59241-T1
Valid prediction for GlimmerHMM_glimmerT_59231-T1
Valid prediction for snap_scaffold_28-snap.1857-T1
Valid prediction for snap_scaffold_28-snap.1876-T1
Valid prediction for snap_scaffold_28-snap.1865-T1
Valid prediction for Augustus_model.g39262.t1
Valid prediction for CodingQuarry_transcript_43739-T1
Valid prediction for Augustus_model.g39264.t1
Valid prediction for snap_scaffold_28-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_59244-T1
Valid prediction for snap_scaffold_28-snap.1880-T1
Valid prediction for snap_scaffold_28-snap.1874-T1
Couldn't classify 48694, 48970
Couldn't classify 49141, 49199
Sorry, prediction pasa_asmbl_38595.p1 fails validation.
(TCC)	 CA	48694-48970	GT	AGG
(GGG)	 AG	49141-49199	AC	CCA
Couldn't classify 17066, 17170
Sorry, prediction pasa_asmbl_38452.p2 fails validation.
(AGA)	 GG	17066-17170	GT	TGG
(ACT)	 AG	17686-17739	GT	GTG
(ATC)	 AG	18445-18550	GT	TGG
(GCG)	 AG	18687-18835	AC	AAA
-recovered pasa_asmbl_38452.p2, terminal, 18687, 18835
-recovered pasa_asmbl_38452.p2, internal, 17686, 17739
-recovered pasa_asmbl_38452.p2, internal, 18445, 18550
Valid prediction for GlimmerHMM_glimmerT_59249-T1
Valid prediction for HiQ_model.g39266.t1
Valid prediction for Augustus_model.g39263.t1
Valid prediction for Augustus_model.g39252.t1
Valid prediction for snap_scaffold_28-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_59240-T1
Valid prediction for HiQ_model.g39265.t1
Valid prediction for CodingQuarry_transcript_43738-T1
Valid prediction for GlimmerHMM_glimmerT_59246-T1
Valid prediction for pasa_asmbl_38453.p1
Valid prediction for GlimmerHMM_glimmerT_59230-T1
Valid prediction for snap_scaffold_28-snap.1851-T1
Valid prediction for GlimmerHMM_glimmerT_59238-T1
Valid prediction for snap_scaffold_28-snap.1881-T1
Valid prediction for snap_scaffold_28-snap.1871-T1
Couldn't classify 34742, 34807
Couldn't classify 36593, 36612
Sorry, prediction pasa_asmbl_38556.p1 fails validation.
(TTC)	 CC	34742-34807	GT	AGG
(TCA)	 AG	36043-36207	GT	TGG
(TCC)	 AG	36320-36398	GT	AGG
(GCC)	 AG	36593-36612	GA	CAG
add_exon() Sorry, pasa_asmbl_38556.p1 36320-36398-terminal-3 is invalid.
-recovered pasa_asmbl_38556.p1, terminal, 36320, 36398
-recovered pasa_asmbl_38556.p1, internal, 36043, 36207
-recovered pasa_asmbl_38556.p1, internal, 36320, 36398
Valid prediction for Augustus_model.g39261.t1
Valid prediction for snap_scaffold_28-snap.1875-T1
Valid prediction for snap_scaffold_28-snap.1855-T1
Valid prediction for snap_scaffold_28-snap.1879-T1
Valid prediction for snap_scaffold_28-snap.1868-T1
Valid prediction for GlimmerHMM_glimmerT_59250-T1
Valid prediction for snap_scaffold_28-snap.1853-T1
Valid prediction for snap_scaffold_28-snap.1859-T1
Valid prediction for snap_scaffold_28-snap.1867-T1
Valid prediction for Augustus_model.g39251.t1
Valid prediction for GlimmerHMM_glimmerT_59243-T1
Valid prediction for GlimmerHMM_glimmerT_59245-T1
Valid prediction for Augustus_model.g39256.t1
Valid prediction for Augustus_model.g39258.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10027, rend_intergenic: 7140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23791, rend_intergenic: 18646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29575, rend_intergenic: 25894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31316, rend_intergenic: 30175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42761, rend_intergenic: 34384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53021, rend_intergenic: 51973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57223, rend_intergenic: 53642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59875, rend_intergenic: 57392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66926, rend_intergenic: 64366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94780, rend_intergenic: 93052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117375, rend_intergenic: 103331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 118966
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 10027, rend_intergenic: 7140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23791, rend_intergenic: 18646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29575, rend_intergenic: 25894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31316, rend_intergenic: 30175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42761, rend_intergenic: 34384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53021, rend_intergenic: 51973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57223, rend_intergenic: 53642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59875, rend_intergenic: 57392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66926, rend_intergenic: 64366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94780, rend_intergenic: 93052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117375, rend_intergenic: 103331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support