-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_16833235-16979970

-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.g1665.t1
Valid prediction for CodingQuarry_transcript_2969-T1
Valid prediction for snap_scaffold_1-snap.3011-T1
Valid prediction for Augustus_model.g1659.t1
Valid prediction for GlimmerHMM_glimmerT_2240-T1
Valid prediction for GlimmerHMM_glimmerT_2245-T1
Valid prediction for snap_scaffold_1-snap.3017-T1
Valid prediction for GlimmerHMM_glimmerT_2239-T1
Valid prediction for Augustus_model.g1668.t1
Valid prediction for Augustus_model.g1660.t1
Valid prediction for HiQ_model.g1658.t1
Couldn't classify 38460, 38555
Couldn't classify 40679, 40709
Sorry, prediction pasa_asmbl_2511.p1 fails validation.
(GTT)	 AG	38460-38555	GT	CGG
(GTG)	 AG	39831-39917	GT	AGG
(CTT)	 AG	40106-40165	GT	CGG
(GTG)	 AG	40289-40422	GT	ACG
(TGA)	 AG	40679-40709	GC	GAG
-recovered pasa_asmbl_2511.p1, internal, 38460, 38555
-recovered pasa_asmbl_2511.p1, internal, 39831, 39917
-recovered pasa_asmbl_2511.p1, internal, 40106, 40165
-recovered pasa_asmbl_2511.p1, internal, 40289, 40422
-recovered pasa_asmbl_2511.p1, internal, 40679, 40709
Valid prediction for snap_scaffold_1-snap.3007-T1
Valid prediction for snap_scaffold_1-snap.3006-T1
Valid prediction for GlimmerHMM_glimmerT_2236-T1
Valid prediction for snap_scaffold_1-snap.3012-T1
Valid prediction for CodingQuarry_transcript_2968-T1
Valid prediction for snap_scaffold_1-snap.3008-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3009-T1
Valid prediction for snap_scaffold_1-snap.3000-T1
Valid prediction for Augustus_model.g1662.t1
Valid prediction for pasa_asmbl_2509.p1
Valid prediction for snap_scaffold_1-snap.3021-T1
Valid prediction for Augustus_model.g1661.t1
Couldn't classify 24597, 24671
Sorry, prediction pasa_asmbl_2715.p1 fails validation.
(ATG)	 AG	23809-23940	GT	AGG
(CTG)	 AG	24033-24212	GT	AGG
(ATT)	 AG	24597-24671	GT	CTG
-recovered pasa_asmbl_2715.p1, initial, 23809, 23940
-recovered pasa_asmbl_2715.p1, internal, 23809, 23940
-recovered pasa_asmbl_2715.p1, internal, 24033, 24212
-recovered pasa_asmbl_2715.p1, internal, 24597, 24671
Valid prediction for snap_scaffold_1-snap.3003-T1
Valid prediction for snap_scaffold_1-snap.3002-T1
Valid prediction for snap_scaffold_1-snap.3004-T1
Valid prediction for GlimmerHMM_glimmerT_2251-T1
Valid prediction for GlimmerHMM_glimmerT_2232-T1
Valid prediction for snap_scaffold_1-snap.3029-T1
Valid prediction for GlimmerHMM_glimmerT_2247-T1
Valid prediction for GlimmerHMM_glimmerT_2234-T1
Valid prediction for GlimmerHMM_glimmerT_2237-T1
Valid prediction for Augustus_model.g1663.t1
Valid prediction for snap_scaffold_1-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_2242-T1
Couldn't classify 18122, 19807
Sorry, prediction pasa_asmbl_2510.p1 fails validation.
(CGG)	 TT	18122-19807	CT	AAC

-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_1-snap.3024-T1
Valid prediction for snap_scaffold_1-snap.3020-T1
Valid prediction for Augustus_model.g1657.t1
Valid prediction for snap_scaffold_1-snap.3030-T1
Valid prediction for GlimmerHMM_glimmerT_2244-T1
Valid prediction for snap_scaffold_1-snap.3027-T1
Valid prediction for snap_scaffold_1-snap.3001-T1
Valid prediction for pasa_asmbl_1021.p1
Valid prediction for snap_scaffold_1-snap.3018-T1
Valid prediction for GlimmerHMM_glimmerT_2250-T1
Valid prediction for GlimmerHMM_glimmerT_2241-T1
Valid prediction for GlimmerHMM_glimmerT_2248-T1
Valid prediction for snap_scaffold_1-snap.3010-T1
Valid prediction for CodingQuarry_transcript_2970-T1
Valid prediction for snap_scaffold_1-snap.3016-T1
Valid prediction for snap_scaffold_1-snap.3014-T1
Valid prediction for Augustus_model.g1667.t1
Valid prediction for snap_scaffold_1-snap.3026-T1
Valid prediction for GlimmerHMM_glimmerT_2243-T1
Valid prediction for GlimmerHMM_glimmerT_2238-T1
Valid prediction for snap_scaffold_1-snap.3013-T1
Valid prediction for GlimmerHMM_glimmerT_2249-T1
Valid prediction for GlimmerHMM_glimmerT_2246-T1
Valid prediction for snap_scaffold_1-snap.3019-T1
Valid prediction for snap_scaffold_1-snap.3028-T1
Valid prediction for GlimmerHMM_glimmerT_2233-T1
Valid prediction for Augustus_model.g1669.t1
Valid prediction for Augustus_model.g1664.t1
Valid prediction for snap_scaffold_1-snap.3023-T1
Valid prediction for snap_scaffold_1-snap.3015-T1
Valid prediction for snap_scaffold_1-snap.3005-T1
Couldn't classify 43556, 43921
Sorry, prediction pasa_asmbl_1023.p2 fails validation.
(CCT)	 TT	43556-43921	GT	GAG
Valid prediction for Augustus_model.g1666.t1
Valid prediction for snap_scaffold_1-snap.3022-T1
Valid prediction for GlimmerHMM_glimmerT_2235-T1
Couldn't classify 141361, 141523
Sorry, prediction pasa_asmbl_1019.p1 fails validation.
(ATG)	 AG	140482-140611	GT	CGG
(GGA)	 AG	140772-140871	GT	TTG
(GTC)	 AG	141015-141167	GT	AGG
(GAT)	 AG	141361-141523	AG	CCA
-recovered pasa_asmbl_1019.p1, initial, 140482, 140611
-recovered pasa_asmbl_1019.p1, internal, 140482, 140611
-recovered pasa_asmbl_1019.p1, internal, 140772, 140871
-recovered pasa_asmbl_1019.p1, internal, 141015, 141167

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26240, rend_intergenic: 23809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52754, rend_intergenic: 44968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63847, rend_intergenic: 53600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70977, rend_intergenic: 66479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87771, rend_intergenic: 71014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96270, rend_intergenic: 90807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118007, rend_intergenic: 114053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137543, rend_intergenic: 119120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143198, rend_intergenic: 140650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146736
-exon list size: 339


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 26240, rend_intergenic: 23809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52754, rend_intergenic: 44968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63847, rend_intergenic: 53600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70977, rend_intergenic: 66479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87771, rend_intergenic: 71014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96270, rend_intergenic: 90807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118007, rend_intergenic: 114053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137543, rend_intergenic: 119120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143198, rend_intergenic: 140650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 122831 - 146736
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 4 predictions from path traversal

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