-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_10729859-11023031

-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_4498-T1
Valid prediction for snap_scaffold_2-snap.2141-T1
Valid prediction for Augustus_model.g3018.t1
Valid prediction for Augustus_model.g3000.t1
Valid prediction for snap_scaffold_2-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_4507-T1
Valid prediction for snap_scaffold_2-snap.2128-T1
Valid prediction for snap_scaffold_2-snap.2111-T1
Valid prediction for snap_scaffold_2-snap.2110-T1
Valid prediction for HiQ_model.g3019.t1
Valid prediction for GlimmerHMM_glimmerT_4504-T1
Valid prediction for snap_scaffold_2-snap.2132-T1
Valid prediction for Augustus_model.g3017.t1
Valid prediction for GlimmerHMM_glimmerT_4500-T1
Valid prediction for GlimmerHMM_glimmerT_4505-T1
Valid prediction for pasa_asmbl_24739.p2
Couldn't classify 30546, 30656
Sorry, prediction pasa_asmbl_24731.p1 fails validation.
(AGC)	 CC	30546-30656	GT	AAG
(GTG)	 AG	30860-30976	GT	AGG
(TTG)	 AG	31348-31443	GC	AAG
-recovered pasa_asmbl_24731.p1, terminal, 31348, 31443
-recovered pasa_asmbl_24731.p1, internal, 30860, 30976
-recovered pasa_asmbl_24731.p1, internal, 31348, 31443
Couldn't classify 139530, 139648
Couldn't classify 142819, 143009
Sorry, prediction pasa_asmbl_24742.p1 fails validation.
(GAG)	 AG	139530-139648	GT	AGG
(GCC)	 AG	140432-140490	GT	AGG
(ACA)	 AG	142819-143009	CT	GCC
-recovered pasa_asmbl_24742.p1, internal, 139530, 139648
-recovered pasa_asmbl_24742.p1, internal, 140432, 140490
Valid prediction for Augustus_model.g3022.t1
Valid prediction for GlimmerHMM_glimmerT_4501-T1
Couldn't classify 139530, 139648
Sorry, prediction pasa_asmbl_24741.p1 fails validation.
(GAG)	 AG	139530-139648	GT	AGG
(GCC)	 AG	140432-140490	GT	AGG
(ACA)	 AG	142819-142951	GT	AGG
(GTT)	 AG	145669-145694	GT	AAG
(AGA)	 AG	145890-145981	GT	TTG
(ATC)	 AG	146842-146933	GT	AGG
(AGG)	 AG	147118-147166	GT	AGG
(GAA)	 AG	147432-147503	GT	AGG
(AAC)	 AG	147642-147685	GT	AAG
(CCT)	 AG	147851-147960	GT	GGG
(GTC)	 AG	148289-148443	GT	GGG
(CTC)	 AG	148822-148839	GT	AGG
(ATT)	 AG	150269-150416	GT	TGG
(TGT)	 AG	150648-150741	GT	AAG
(TTA)	 AG	150995-151085	GT	AGG
(TAC)	 AG	151225-151293	GT	AGG
(CCT)	 AG	151577-151684	CC	AGC
add_exon() Sorry, pasa_asmbl_24741.p1 145669-145694-terminal-2 is invalid.
-recovered pasa_asmbl_24741.p1, terminal, 145669, 145694
-recovered pasa_asmbl_24741.p1, terminal, 151577, 151684
-recovered pasa_asmbl_24741.p1, internal, 139530, 139648
-recovered pasa_asmbl_24741.p1, internal, 140432, 140490
-recovered pasa_asmbl_24741.p1, internal, 142819, 142951
-recovered pasa_asmbl_24741.p1, internal, 145669, 145694
-recovered pasa_asmbl_24741.p1, internal, 145890, 145981
-recovered pasa_asmbl_24741.p1, internal, 146842, 146933
-recovered pasa_asmbl_24741.p1, internal, 147118, 147166
-recovered pasa_asmbl_24741.p1, internal, 147432, 147503
-recovered pasa_asmbl_24741.p1, internal, 147642, 147685
-recovered pasa_asmbl_24741.p1, internal, 147851, 147960
-recovered pasa_asmbl_24741.p1, internal, 148289, 148443
-recovered pasa_asmbl_24741.p1, internal, 148822, 148839
-recovered pasa_asmbl_24741.p1, internal, 150269, 150416
-recovered pasa_asmbl_24741.p1, internal, 150648, 150741
-recovered pasa_asmbl_24741.p1, internal, 150995, 151085
-recovered pasa_asmbl_24741.p1, internal, 151225, 151293
Valid prediction for snap_scaffold_2-snap.2108-T1
Valid prediction for GlimmerHMM_glimmerT_4483-T1
Valid prediction for Augustus_model.g3004.t1
Valid prediction for snap_scaffold_2-snap.2112-T1
Valid prediction for Augustus_model.g3002.t1
Valid prediction for snap_scaffold_2-snap.2129-T1
Valid prediction for Augustus_model.g3003.t1
Valid prediction for snap_scaffold_2-snap.2137-T1
Valid prediction for snap_scaffold_2-snap.2109-T1
Valid prediction for snap_scaffold_2-snap.2113-T1
Valid prediction for snap_scaffold_2-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_4482-T1
Valid prediction for Augustus_model.g3001.t1
Valid prediction for snap_scaffold_2-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_4481-T1
Valid prediction for GlimmerHMM_glimmerT_4496-T1
Valid prediction for snap_scaffold_2-snap.2145-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_2-snap.2114-T1
Valid prediction for snap_scaffold_2-snap.2123-T1
Valid prediction for Augustus_model.g3016.t1
Valid prediction for Augustus_model.g3008.t1
Valid prediction for snap_scaffold_2-snap.2118-T1
Valid prediction for snap_scaffold_2-snap.2125-T1
Valid prediction for snap_scaffold_2-snap.2116-T1
Valid prediction for Augustus_model.g3014.t1
Valid prediction for Augustus_model.g3013.t1
Valid prediction for Augustus_model.g3012.t1
Valid prediction for snap_scaffold_2-snap.2130-T1
Valid prediction for Augustus_model.g3006.t1
Valid prediction for GlimmerHMM_glimmerT_4503-T1
Valid prediction for Augustus_model.g3007.t1
Valid prediction for snap_scaffold_2-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_4489-T1
Valid prediction for snap_scaffold_2-snap.2119-T1
Valid prediction for Augustus_model.g3023.t1
Valid prediction for GlimmerHMM_glimmerT_4484-T1
Valid prediction for GlimmerHMM_glimmerT_4497-T1
Valid prediction for snap_scaffold_2-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_4491-T1
Valid prediction for Augustus_model.g3009.t1
Valid prediction for GlimmerHMM_glimmerT_4493-T1
Valid prediction for GlimmerHMM_glimmerT_4487-T1
Valid prediction for pasa_asmbl_23441.p1
Valid prediction for Augustus_model.g3011.t1
Valid prediction for GlimmerHMM_glimmerT_4499-T1
Valid prediction for snap_scaffold_2-snap.2115-T1
Valid prediction for snap_scaffold_2-snap.2121-T1
Valid prediction for Augustus_model.g3010.t1
Valid prediction for snap_scaffold_2-snap.2138-T1
Valid prediction for snap_scaffold_2-snap.2126-T1
Valid prediction for snap_scaffold_2-snap.2144-T1
Valid prediction for snap_scaffold_2-snap.2120-T1
Valid prediction for snap_scaffold_2-snap.2139-T1
Valid prediction for Augustus_model.g3005.t1
Valid prediction for GlimmerHMM_glimmerT_4488-T1
Valid prediction for snap_scaffold_2-snap.2140-T1
Valid prediction for snap_scaffold_2-snap.2142-T1
Valid prediction for GlimmerHMM_glimmerT_4508-T1
Valid prediction for GlimmerHMM_glimmerT_4486-T1
Valid prediction for GlimmerHMM_glimmerT_4490-T1
Valid prediction for Augustus_model.g3015.t1
Valid prediction for snap_scaffold_2-snap.2133-T1
Valid prediction for HiQ_model.g3021.t1
Valid prediction for snap_scaffold_2-snap.2134-T1
Valid prediction for snap_scaffold_2-snap.2146-T1
Valid prediction for GlimmerHMM_glimmerT_4494-T1
Valid prediction for GlimmerHMM_glimmerT_4492-T1
Valid prediction for snap_scaffold_2-snap.2117-T1
Valid prediction for Augustus_model.g3020.t1
Valid prediction for GlimmerHMM_glimmerT_4506-T1
Valid prediction for snap_scaffold_2-snap.2124-T1
Valid prediction for snap_scaffold_2-snap.2122-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4495-T1
Valid prediction for GlimmerHMM_glimmerT_4485-T1
Valid prediction for GlimmerHMM_glimmerT_4502-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 151684, rend_intergenic: 137958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164065, rend_intergenic: 160014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199188, rend_intergenic: 192456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227644, rend_intergenic: 224940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 284841, rend_intergenic: 282908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 293173
-exon list size: 344


building trellis

0.3    
0.6    
0.9    
1.2    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 151684, rend_intergenic: 137958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164065, rend_intergenic: 160014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199188, rend_intergenic: 192456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227644, rend_intergenic: 224940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 284841, rend_intergenic: 282908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10579
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 244319 - 293173
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 244319 - 284835
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 244319 - 282907
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 244319 - 259915
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 244319 - 254416
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 259984 - 282907
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 259984 - 281867
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 259984 - 272022
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support