-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_734758-875979

-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.189-T1
Valid prediction for GlimmerHMM_glimmerT_8686-T1
Valid prediction for snap_scaffold_4-snap.191-T1
Valid prediction for snap_scaffold_4-snap.186-T1
Valid prediction for GlimmerHMM_glimmerT_8671-T1
Valid prediction for snap_scaffold_4-snap.183-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8680-T1
Valid prediction for snap_scaffold_4-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_8679-T1
Valid prediction for GlimmerHMM_glimmerT_8676-T1
Valid prediction for GlimmerHMM_glimmerT_8685-T1
Valid prediction for snap_scaffold_4-snap.180-T1
Valid prediction for GlimmerHMM_glimmerT_8669-T1
Valid prediction for snap_scaffold_4-snap.160-T1
Valid prediction for Augustus_model.g5631.t1
Valid prediction for snap_scaffold_4-snap.192-T1
Valid prediction for snap_scaffold_4-snap.177-T1
Valid prediction for GlimmerHMM_glimmerT_8683-T1
Valid prediction for snap_scaffold_4-snap.169-T1
Valid prediction for snap_scaffold_4-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_8674-T1
Valid prediction for snap_scaffold_4-snap.175-T1
Valid prediction for GlimmerHMM_glimmerT_8688-T1
Valid prediction for GlimmerHMM_glimmerT_8681-T1
Valid prediction for snap_scaffold_4-snap.167-T1
Valid prediction for snap_scaffold_4-snap.171-T1
Valid prediction for snap_scaffold_4-snap.174-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8677-T1
Valid prediction for snap_scaffold_4-snap.162-T1
Valid prediction for snap_scaffold_4-snap.187-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 Augustus_model.g5628.t1
Valid prediction for snap_scaffold_4-snap.163-T1
Valid prediction for snap_scaffold_4-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_8670-T1
Valid prediction for snap_scaffold_4-snap.172-T1
Valid prediction for snap_scaffold_4-snap.159-T1
Valid prediction for snap_scaffold_4-snap.181-T1
Valid prediction for Augustus_model.g5629.t1
Valid prediction for Augustus_model.g5627.t1
Valid prediction for snap_scaffold_4-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_8684-T1
Valid prediction for GlimmerHMM_glimmerT_8678-T1
Valid prediction for GlimmerHMM_glimmerT_8673-T1
Couldn't classify 108194, 108238
Couldn't classify 111152, 111310
Sorry, prediction pasa_asmbl_42348.p1 fails validation.
(CTC)	 TC	108194-108238	GT	AGG
(GTG)	 AG	108522-108615	GT	GCG
(ACC)	 AG	110283-110398	GT	AGG
(GCT)	 AG	111152-111310	CA	GGC
-recovered pasa_asmbl_42348.p1, internal, 108522, 108615
-recovered pasa_asmbl_42348.p1, internal, 110283, 110398
Valid prediction for GlimmerHMM_glimmerT_8667-T1
Valid prediction for snap_scaffold_4-snap.188-T1
Valid prediction for Augustus_model.g5630.t1
Valid prediction for snap_scaffold_4-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_8687-T1
Valid prediction for snap_scaffold_4-snap.179-T1
Valid prediction for snap_scaffold_4-snap.173-T1
Valid prediction for snap_scaffold_4-snap.165-T1
Valid prediction for snap_scaffold_4-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_8682-T1
Valid prediction for snap_scaffold_4-snap.178-T1
Valid prediction for snap_scaffold_4-snap.184-T1
Valid prediction for snap_scaffold_4-snap.166-T1
Valid prediction for snap_scaffold_4-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_8675-T1
Valid prediction for GlimmerHMM_glimmerT_8689-T1
Valid prediction for snap_scaffold_4-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_8668-T1
Valid prediction for snap_scaffold_4-snap.157-T1
Valid prediction for CodingQuarry_transcript_48870-T1
Valid prediction for GlimmerHMM_glimmerT_8672-T1
Valid prediction for snap_scaffold_4-snap.170-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5625, rend_intergenic: 2800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7624, rend_intergenic: 7037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10256, rend_intergenic: 7781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10726, rend_intergenic: 10350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26351, rend_intergenic: 11163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34519, rend_intergenic: 26403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45824, rend_intergenic: 35489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49026, rend_intergenic: 46388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52379, rend_intergenic: 49120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61544, rend_intergenic: 56796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74266, rend_intergenic: 62947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76983, rend_intergenic: 75083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95671, rend_intergenic: 89350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97173, rend_intergenic: 95859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105478, rend_intergenic: 98777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121457, rend_intergenic: 106071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126341, rend_intergenic: 121851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127209, rend_intergenic: 126752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131497, rend_intergenic: 127816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139496, rend_intergenic: 133043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 141222
-exon list size: 239


building trellis

0.4    
0.8    
1.2    
1.7    
2.1    
2.5    
2.9    
3.3    
3.7    
4.1    
4.6    
5.0    
5.4    
5.8    
6.2    
6.6    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
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10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
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13.3    
13.7    
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16.2    
16.6    
17.0    
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17.8    
18.3    
18.7    
19.1    
19.5    
19.9    
20.3    
20.7    
21.2    
21.6    
22.0    
22.4    
22.8    
23.2    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.6    
27.0    
27.4    
27.8    
28.2    
28.6    
29.0    
29.5    
29.9    
30.3    
30.7    
31.1    
31.5    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.8    
38.2    
38.6    
39.0    
39.4    
39.8    
40.2    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
46.1    
46.5    
46.9    
47.3    
47.7    
48.1    
48.5    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.5    
51.9    
52.3    
52.7    
53.1    
53.5    
53.9    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.8    
60.2    
60.6    
61.0    
61.4    
61.8    
62.2    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.5    
68.9    
69.3    
69.7    
70.1    
70.5    
71.0    
71.4    
71.8    
72.2    
72.6    
73.0    
73.4    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.3    
79.7    
80.1    
80.5    
80.9    
81.3    
81.7    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.4    
93.8    
94.2    
94.6    
95.0    
95.4    
95.9    
96.3    
96.7    
97.1    
97.5    
97.9    
98.3    
98.8    
99.2    
99.6    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 5625, rend_intergenic: 2800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7624, rend_intergenic: 7037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10256, rend_intergenic: 7781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10726, rend_intergenic: 10350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26351, rend_intergenic: 11163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34519, rend_intergenic: 26403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45824, rend_intergenic: 35489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49026, rend_intergenic: 46388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52379, rend_intergenic: 49120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61544, rend_intergenic: 56796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74266, rend_intergenic: 62947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76983, rend_intergenic: 75083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95671, rend_intergenic: 89350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97173, rend_intergenic: 95859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105478, rend_intergenic: 98777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121457, rend_intergenic: 106071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126341, rend_intergenic: 121851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127209, rend_intergenic: 126752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131497, rend_intergenic: 127816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139496, rend_intergenic: 133043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support