-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_9706290-9881120

-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_4-snap.2059-T1
Couldn't classify 124169, 124443
Couldn't classify 124773, 124818
Sorry, prediction pasa_asmbl_42285.p2 fails validation.
(CAC)	 AA	124169-124443	GT	AGG
(ACC)	 AG	124773-124818	GT	CCG
-recovered pasa_asmbl_42285.p2, internal, 124773, 124818
Valid prediction for GlimmerHMM_glimmerT_9998-T1
Valid prediction for snap_scaffold_4-snap.2074-T1
Valid prediction for snap_scaffold_4-snap.2065-T1
Valid prediction for snap_scaffold_4-snap.2089-T1
Valid prediction for Augustus_model.g6487.t1
Valid prediction for Augustus_model.g6488.t1
Valid prediction for GlimmerHMM_glimmerT_9995-T1
Valid prediction for GlimmerHMM_glimmerT_9971-T1
Valid prediction for Augustus_model.g6491.t1
Valid prediction for GlimmerHMM_glimmerT_9973-T1
Valid prediction for snap_scaffold_4-snap.2060-T1
Valid prediction for Augustus_model.g6490.t1
Valid prediction for Augustus_model.g6484.t1
Valid prediction for Augustus_model.g6482.t1
Valid prediction for GlimmerHMM_glimmerT_9992-T1
Valid prediction for snap_scaffold_4-snap.2063-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.2085-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9997-T1
Valid prediction for GlimmerHMM_glimmerT_9977-T1
Valid prediction for GlimmerHMM_glimmerT_9988-T1
Valid prediction for snap_scaffold_4-snap.2077-T1
Valid prediction for snap_scaffold_4-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_9974-T1
Valid prediction for Augustus_model.g6496.t1
Valid prediction for snap_scaffold_4-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_9980-T1
Valid prediction for Augustus_model.g6479.t1
Couldn't classify 127956, 128050
Sorry, prediction pasa_asmbl_41626.p1 fails validation.
(GGG)	 GT	127956-128050	GT	CAG
(CTG)	 AG	128277-128338	GT	GAG
(CGC)	 AG	128500-128652	GT	GGG
(AGC)	 AG	128813-128949	GT	TGG
(GTG)	 AG	129120-129175	GT	AGG
(GAC)	 AG	129328-129492	GT	ATG
(GTA)	 AG	129732-129861	GT	AGG
(AAG)	 AG	130459-130761	AT	GAA
add_exon() Sorry, pasa_asmbl_41626.p1 128277-128338-terminal-2 is invalid.
-recovered pasa_asmbl_41626.p1, terminal, 128277, 128338
-recovered pasa_asmbl_41626.p1, terminal, 130459, 130761
-recovered pasa_asmbl_41626.p1, internal, 128277, 128338
-recovered pasa_asmbl_41626.p1, internal, 128500, 128652
-recovered pasa_asmbl_41626.p1, internal, 128813, 128949
-recovered pasa_asmbl_41626.p1, internal, 129120, 129175
-recovered pasa_asmbl_41626.p1, internal, 129328, 129492
-recovered pasa_asmbl_41626.p1, internal, 129732, 129861
Valid prediction for Augustus_model.g6495.t1
Couldn't classify 26068, 26178
Sorry, prediction pasa_asmbl_41620.p1 fails validation.
(ATG)	 GG	18832-19000	GT	TGG
(GCC)	 AG	19559-19636	GT	AGG
(TGA)	 AG	19781-19849	GT	TGG
(GTA)	 AG	22430-22563	GT	AGG
(ATA)	 AG	23288-23443	GT	AGG
(GTG)	 AG	24302-24410	GT	AGG
(TGG)	 AG	25352-25449	GT	AGG
(GTT)	 AG	26068-26178	GT	AGG
-recovered pasa_asmbl_41620.p1, initial, 18832, 19000
-recovered pasa_asmbl_41620.p1, internal, 19559, 19636
-recovered pasa_asmbl_41620.p1, internal, 19781, 19849
-recovered pasa_asmbl_41620.p1, internal, 22430, 22563
-recovered pasa_asmbl_41620.p1, internal, 23288, 23443
-recovered pasa_asmbl_41620.p1, internal, 24302, 24410
-recovered pasa_asmbl_41620.p1, internal, 25352, 25449
-recovered pasa_asmbl_41620.p1, internal, 26068, 26178
Couldn't classify 64839, 65141
Sorry, prediction pasa_asmbl_42822.p1 fails validation.
(GGG)	 GA	64839-65141	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_9979-T1
Valid prediction for Augustus_model.g6481.t1
Valid prediction for snap_scaffold_4-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_9978-T1
Valid prediction for Augustus_model.g6494.t1
Valid prediction for snap_scaffold_4-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_9994-T1
Valid prediction for snap_scaffold_4-snap.2071-T1
Valid prediction for snap_scaffold_4-snap.2072-T1
Valid prediction for snap_scaffold_4-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_9999-T1
Valid prediction for GlimmerHMM_glimmerT_9996-T1
Valid prediction for Augustus_model.g6492.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_4-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_9987-T1
Valid prediction for snap_scaffold_4-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_9975-T1
Valid prediction for snap_scaffold_4-snap.2091-T1
Valid prediction for snap_scaffold_4-snap.2067-T1
Valid prediction for snap_scaffold_4-snap.2083-T1
Valid prediction for Augustus_model.g6486.t1
Valid prediction for GlimmerHMM_glimmerT_9985-T1
Valid prediction for Augustus_model.g6493.t1
Valid prediction for snap_scaffold_4-snap.2068-T1
Valid prediction for snap_scaffold_4-snap.2079-T1
Valid prediction for Augustus_model.g6480.t1
Valid prediction for snap_scaffold_4-snap.2086-T1
Valid prediction for snap_scaffold_4-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_10002-T1
Valid prediction for GlimmerHMM_glimmerT_9982-T1
Valid prediction for CodingQuarry_transcript_49100-T1
Valid prediction for snap_scaffold_4-snap.2064-T1
Valid prediction for HiQ_model.g6489.t1
Valid prediction for snap_scaffold_4-snap.2076-T1
Valid prediction for Augustus_model.g6497.t1
Valid prediction for snap_scaffold_4-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_9976-T1
Valid prediction for GlimmerHMM_glimmerT_10000-T1
Couldn't classify 108702, 109370
Sorry, prediction pasa_asmbl_42823.p1 fails validation.
(ATG)	 CA	107820-108251	GT	AGG
(GAG)	 AG	108702-109370	CC	AGC
-recovered pasa_asmbl_42823.p1, initial, 107820, 108251
Valid prediction for GlimmerHMM_glimmerT_9972-T1
Valid prediction for snap_scaffold_4-snap.2090-T1
Valid prediction for snap_scaffold_4-snap.2070-T1
Valid prediction for Augustus_model.g6485.t1
Valid prediction for snap_scaffold_4-snap.2058-T1
Valid prediction for GlimmerHMM_glimmerT_9981-T1
Valid prediction for snap_scaffold_4-snap.2073-T1
Valid prediction for GlimmerHMM_glimmerT_9984-T1
Valid prediction for GlimmerHMM_glimmerT_9990-T1
Valid prediction for GlimmerHMM_glimmerT_9989-T1
Valid prediction for GlimmerHMM_glimmerT_9991-T1
Valid prediction for GlimmerHMM_glimmerT_10001-T1
Valid prediction for snap_scaffold_4-snap.2078-T1
Valid prediction for snap_scaffold_4-snap.2066-T1
Valid prediction for pasa_asmbl_42825.p1
Valid prediction for snap_scaffold_4-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_9983-T1
Valid prediction for pasa_asmbl_42820.p1
Valid prediction for GlimmerHMM_glimmerT_9993-T1
Valid prediction for snap_scaffold_4-snap.2093-T1
Valid prediction for Augustus_model.g6483.t1
Valid prediction for snap_scaffold_4-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_9986-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28556, rend_intergenic: 22426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45248, rend_intergenic: 32351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51702, rend_intergenic: 48579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61196, rend_intergenic: 56090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62750, rend_intergenic: 61982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74611, rend_intergenic: 72647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85556, rend_intergenic: 74844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95573, rend_intergenic: 91449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101587, rend_intergenic: 97986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110741, rend_intergenic: 103170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130761, rend_intergenic: 113661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141016, rend_intergenic: 132525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154544, rend_intergenic: 143888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167544, rend_intergenic: 162844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173040, rend_intergenic: 169438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174831
-exon list size: 521


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
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    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
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    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
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    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
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    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 28556, rend_intergenic: 22426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45248, rend_intergenic: 32351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51702, rend_intergenic: 48579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61196, rend_intergenic: 56090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62750, rend_intergenic: 61982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74611, rend_intergenic: 72647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85556, rend_intergenic: 74844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95573, rend_intergenic: 91449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101587, rend_intergenic: 97986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110741, rend_intergenic: 103170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130761, rend_intergenic: 113661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141016, rend_intergenic: 132525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154544, rend_intergenic: 143888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167544, rend_intergenic: 162844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173040, rend_intergenic: 169438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support