-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_3618099-3829309

-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.g17774.t1
Valid prediction for snap_scaffold_11-snap.929-T1
Valid prediction for snap_scaffold_11-snap.901-T1
Valid prediction for snap_scaffold_11-snap.916-T1
Valid prediction for snap_scaffold_11-snap.905-T1
Valid prediction for Augustus_model.g17795.t1
Valid prediction for snap_scaffold_11-snap.908-T1
Valid prediction for snap_scaffold_11-snap.911-T1
Valid prediction for GlimmerHMM_glimmerT_26878-T1
Valid prediction for Augustus_model.g17777.t1
Valid prediction for GlimmerHMM_glimmerT_26871-T1
Valid prediction for GlimmerHMM_glimmerT_26893-T1
Valid prediction for snap_scaffold_11-snap.903-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.927-T1
Valid prediction for GlimmerHMM_glimmerT_26900-T1
Valid prediction for snap_scaffold_11-snap.914-T1
Valid prediction for snap_scaffold_11-snap.925-T1
Couldn't classify 80162, 80469
Sorry, prediction pasa_asmbl_5456.p1 fails validation.
(ATG)	 AG	79931-79955	GT	CGG
(AAA)	 AG	80162-80469	CT	GCC
-recovered pasa_asmbl_5456.p1, initial, 79931, 79955
-recovered pasa_asmbl_5456.p1, internal, 79931, 79955
Valid prediction for Augustus_model.g17801.t1
Valid prediction for GlimmerHMM_glimmerT_26897-T1
Valid prediction for GlimmerHMM_glimmerT_26890-T1
Valid prediction for snap_scaffold_11-snap.907-T1
Valid prediction for GlimmerHMM_glimmerT_26883-T1
Valid prediction for snap_scaffold_11-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_26903-T1
Valid prediction for snap_scaffold_11-snap.922-T1
Valid prediction for Augustus_model.g17790.t1
Valid prediction for Augustus_model.g17778.t1
Valid prediction for GlimmerHMM_glimmerT_26874-T1
Valid prediction for GlimmerHMM_glimmerT_26869-T1
Valid prediction for Augustus_model.g17784.t1
Valid prediction for snap_scaffold_11-snap.931-T1
Valid prediction for Augustus_model.g17776.t1
Valid prediction for GlimmerHMM_glimmerT_26868-T1
Valid prediction for snap_scaffold_11-snap.917-T1
Valid prediction for snap_scaffold_11-snap.920-T1
Valid prediction for GlimmerHMM_glimmerT_26889-T1
Valid prediction for Augustus_model.g17780.t1
Valid prediction for GlimmerHMM_glimmerT_26894-T1
Valid prediction for pasa_asmbl_5460.p1
Valid prediction for GlimmerHMM_glimmerT_26872-T1
Valid prediction for snap_scaffold_11-snap.897-T1
Valid prediction for snap_scaffold_11-snap.923-T1
Valid prediction for snap_scaffold_11-snap.899-T1
Valid prediction for Augustus_model.g17798.t1
Valid prediction for snap_scaffold_11-snap.938-T1
Valid prediction for snap_scaffold_11-snap.896-T1
Valid prediction for pasa_asmbl_5458.p1
Valid prediction for snap_scaffold_11-snap.906-T1
Valid prediction for Augustus_model.g17775.t1
Valid prediction for snap_scaffold_11-snap.936-T1
Valid prediction for snap_scaffold_11-snap.894-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 CodingQuarry_transcript_8027-T1
Valid prediction for GlimmerHMM_glimmerT_26885-T1
Valid prediction for snap_scaffold_11-snap.892-T1
Valid prediction for snap_scaffold_11-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_26892-T1
Valid prediction for GlimmerHMM_glimmerT_26873-T1
Valid prediction for Augustus_model.g17802.t1
Valid prediction for CodingQuarry_transcript_8026-T1
Valid prediction for GlimmerHMM_glimmerT_26870-T1
Valid prediction for snap_scaffold_11-snap.910-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_6575.p1
Valid prediction for GlimmerHMM_glimmerT_26867-T1
Couldn't classify 97482, 97751
Couldn't classify 100924, 100954
Sorry, prediction pasa_asmbl_7285.p1 fails validation.
(AGG)	 CC	97482-97751	GT	AGG
(GTG)	 AG	98474-98704	GT	CGG
(GAG)	 AG	98906-98984	GT	CAG
(TCC)	 AG	100527-100752	GT	AGG
(GGA)	 AG	100924-100954	AT	ACA
-recovered pasa_asmbl_7285.p1, internal, 98474, 98704
-recovered pasa_asmbl_7285.p1, internal, 98906, 98984
-recovered pasa_asmbl_7285.p1, internal, 100527, 100752
Valid prediction for GlimmerHMM_glimmerT_26888-T1
Valid prediction for GlimmerHMM_glimmerT_26896-T1
Valid prediction for GlimmerHMM_glimmerT_26898-T1
Valid prediction for GlimmerHMM_glimmerT_26891-T1
Valid prediction for Augustus_model.g17772.t1
Valid prediction for snap_scaffold_11-snap.924-T1
Valid prediction for HiQ_model.g17796.t1
Valid prediction for Augustus_model.g17792.t1
Valid prediction for CodingQuarry_transcript_8024-T1
Valid prediction for snap_scaffold_11-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_26879-T1
Valid prediction for GlimmerHMM_glimmerT_26899-T1
Valid prediction for GlimmerHMM_glimmerT_26886-T1
Valid prediction for GlimmerHMM_glimmerT_26895-T1
Valid prediction for CodingQuarry_transcript_8029-T1
Valid prediction for GlimmerHMM_glimmerT_26877-T1
Couldn't classify 116401, 116562
Sorry, prediction pasa_asmbl_6560.p1 fails validation.
(GTT)	 GA	116401-116562	GT	AGG
(TGC)	 AG	117343-117393	GT	AGG
(CAC)	 AG	117504-117672	GT	GGG
(GTG)	 AG	118282-118357	GT	AGG
(GTA)	 AG	118568-118659	GT	AGG
(GTG)	 AG	119709-119839	GT	AGG
(GCT)	 AG	119999-120034	GA	GAG
-recovered pasa_asmbl_6560.p1, terminal, 119999, 120034
-recovered pasa_asmbl_6560.p1, internal, 117343, 117393
-recovered pasa_asmbl_6560.p1, internal, 117504, 117672
-recovered pasa_asmbl_6560.p1, internal, 118282, 118357
-recovered pasa_asmbl_6560.p1, internal, 118568, 118659
-recovered pasa_asmbl_6560.p1, internal, 119709, 119839
Valid prediction for HiQ_model.g17786.t1
Valid prediction for snap_scaffold_11-snap.909-T1
Valid prediction for CodingQuarry_transcript_8021-T1
Valid prediction for snap_scaffold_11-snap.928-T1
Valid prediction for CodingQuarry_transcript_8030-T1
Valid prediction for HiQ_model.g17773.t1
Valid prediction for snap_scaffold_11-snap.895-T1
Valid prediction for snap_scaffold_11-snap.932-T1
Valid prediction for Augustus_model.g17791.t1
Valid prediction for HiQ_model.g17789.t1
Valid prediction for GlimmerHMM_glimmerT_26881-T1
Valid prediction for HiQ_model.g17799.t1
Valid prediction for GlimmerHMM_glimmerT_26905-T1
Valid prediction for GlimmerHMM_glimmerT_26884-T1
Couldn't classify 29864, 30318
Sorry, prediction pasa_asmbl_6585.p1 fails validation.
(ATG)	 CC	29585-29717	GT	GGG
(AGG)	 AG	29864-30318	GA	TGG
-recovered pasa_asmbl_6585.p1, initial, 29585, 29717
Valid prediction for Augustus_model.g17783.t1
Valid prediction for snap_scaffold_11-snap.902-T1
Valid prediction for CodingQuarry_transcript_8023-T1
Valid prediction for Augustus_model.g17782.t1
Valid prediction for Augustus_model.g17785.t1
Valid prediction for pasa_asmbl_6583.p1
Valid prediction for CodingQuarry_transcript_8025-T1
Valid prediction for GlimmerHMM_glimmerT_26901-T1
Valid prediction for Augustus_model.g17787.t1
Valid prediction for GlimmerHMM_glimmerT_26904-T1
Valid prediction for GlimmerHMM_glimmerT_26902-T1
Valid prediction for snap_scaffold_11-snap.921-T1
Valid prediction for GlimmerHMM_glimmerT_26887-T1
Valid prediction for snap_scaffold_11-snap.918-T1
Valid prediction for CodingQuarry_transcript_8028-T1
Valid prediction for snap_scaffold_11-snap.915-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g17793.t1
Valid prediction for snap_scaffold_11-snap.904-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for pasa_asmbl_6582.p1
Valid prediction for Augustus_model.g17794.t1
Valid prediction for snap_scaffold_11-snap.919-T1
Valid prediction for snap_scaffold_11-snap.912-T1
Couldn't classify 102147, 102248
Couldn't classify 106409, 106615
Sorry, prediction pasa_asmbl_6568.p1 fails validation.
(GTG)	 AG	102147-102248	GT	AGG
(GTT)	 AG	104143-104316	GT	TGG
(GCG)	 AG	104624-104723	GT	TGG
(ATG)	 AG	105099-105151	GT	AGG
(GGG)	 AG	105598-105665	GT	AGG
(CCC)	 AG	105800-105908	GT	AGG
(GGC)	 AG	106409-106615	AC	ACA
-recovered pasa_asmbl_6568.p1, initial, 105099, 105151
-recovered pasa_asmbl_6568.p1, internal, 102147, 102248
-recovered pasa_asmbl_6568.p1, internal, 104143, 104316
-recovered pasa_asmbl_6568.p1, internal, 104624, 104723
-recovered pasa_asmbl_6568.p1, internal, 105099, 105151
-recovered pasa_asmbl_6568.p1, internal, 105598, 105665
-recovered pasa_asmbl_6568.p1, internal, 105800, 105908
Valid prediction for GlimmerHMM_glimmerT_26875-T1
Valid prediction for GlimmerHMM_glimmerT_26882-T1
Valid prediction for snap_scaffold_11-snap.900-T1
Valid prediction for snap_scaffold_11-snap.913-T1
Valid prediction for snap_scaffold_11-snap.933-T1
Valid prediction for CodingQuarry_transcript_8022-T1
Valid prediction for Augustus_model.g17788.t1
Valid prediction for GlimmerHMM_glimmerT_26880-T1
Valid prediction for snap_scaffold_11-snap.898-T1
Valid prediction for Augustus_model.g17800.t1
Valid prediction for HiQ_model.g17797.t1
Valid prediction for pasa_asmbl_6569.p1
Valid prediction for snap_scaffold_11-snap.930-T1
Valid prediction for snap_scaffold_11-snap.934-T1
Valid prediction for Augustus_model.g17781.t1
Valid prediction for GlimmerHMM_glimmerT_26876-T1
Valid prediction for Augustus_model.g17779.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23722, rend_intergenic: 19448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39984, rend_intergenic: 27708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49116, rend_intergenic: 45924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51391, rend_intergenic: 49149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55439, rend_intergenic: 53009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62520, rend_intergenic: 59426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73789, rend_intergenic: 62715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75633, rend_intergenic: 73878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88258, rend_intergenic: 83874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107736, rend_intergenic: 99537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110241, rend_intergenic: 108808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115040, rend_intergenic: 112034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141413, rend_intergenic: 134705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152312, rend_intergenic: 152008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163487, rend_intergenic: 152668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200295, rend_intergenic: 198951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211211
-exon list size: 516


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 23722, rend_intergenic: 19448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39984, rend_intergenic: 27708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49116, rend_intergenic: 45924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51391, rend_intergenic: 49149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55439, rend_intergenic: 53009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62520, rend_intergenic: 59426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73789, rend_intergenic: 62715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75633, rend_intergenic: 73878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88258, rend_intergenic: 83874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107736, rend_intergenic: 99537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110241, rend_intergenic: 108808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115040, rend_intergenic: 112034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141413, rend_intergenic: 134705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152312, rend_intergenic: 152008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163487, rend_intergenic: 152668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200295, rend_intergenic: 198951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support