-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_15998311-16134321

-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_1-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_2104-T1
Couldn't classify 81573, 81821
Couldn't classify 82967, 83119
Sorry, prediction pasa_asmbl_2761.p1 fails validation.
(GAG)	 CC	81573-81821	GT	GGG
(CAC)	 AG	82967-83119	GT	CCG
-recovered pasa_asmbl_2761.p1, internal, 82967, 83119
Valid prediction for GlimmerHMM_glimmerT_2101-T1
Valid prediction for snap_scaffold_1-snap.2810-T1
Valid prediction for GlimmerHMM_glimmerT_2107-T1
Valid prediction for snap_scaffold_1-snap.2793-T1
Valid prediction for snap_scaffold_1-snap.2818-T1
Valid prediction for HiQ_model.g1574.t1
Valid prediction for Augustus_model.g1566.t1
Valid prediction for snap_scaffold_1-snap.2814-T1
Valid prediction for Augustus_model.g1564.t1
Valid prediction for CodingQuarry_transcript_2952-T1
Valid prediction for GlimmerHMM_glimmerT_2108-T1
Valid prediction for snap_scaffold_1-snap.2805-T1
Valid prediction for snap_scaffold_1-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_2103-T1
Valid prediction for Augustus_model.g1570.t1
Valid prediction for Augustus_model.g1567.t1
Valid prediction for HiQ_model.g1575.t1
Valid prediction for snap_scaffold_1-snap.2800-T1
Valid prediction for Augustus_model.g1565.t1
Valid prediction for snap_scaffold_1-snap.2791-T1
Valid prediction for snap_scaffold_1-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_2099-T1
Valid prediction for GlimmerHMM_glimmerT_2097-T1
Valid prediction for GlimmerHMM_glimmerT_2109-T1
Valid prediction for GlimmerHMM_glimmerT_2106-T1
Valid prediction for GlimmerHMM_glimmerT_2102-T1
Valid prediction for Augustus_model.g1571.t1
Valid prediction for GlimmerHMM_glimmerT_2117-T1
Valid prediction for snap_scaffold_1-snap.2807-T1
Valid prediction for GlimmerHMM_glimmerT_2111-T1
Valid prediction for Augustus_model.g1568.t1
Valid prediction for snap_scaffold_1-snap.2803-T1
Valid prediction for snap_scaffold_1-snap.2799-T1
Valid prediction for GlimmerHMM_glimmerT_2100-T1
Valid prediction for Augustus_model.g1569.t1
Couldn't classify 38328, 38394
Couldn't classify 44942, 44964
Sorry, prediction pasa_asmbl_2460.p1 fails validation.
(CCA)	 CA	38328-38394	GT	AAG
(TGA)	 AG	39323-39445	GT	GCG
(TGA)	 AG	42180-42302	GT	AAG
(ACC)	 AG	43044-43166	GT	CAG
(CCT)	 AG	43575-43804	GT	AGG
(GTG)	 AG	43977-44160	GT	AGG
(GTA)	 AG	44280-44432	GT	AGG
(AGG)	 AG	44942-44964	GT	AGG
-recovered pasa_asmbl_2460.p1, internal, 39323, 39445
-recovered pasa_asmbl_2460.p1, internal, 42180, 42302
-recovered pasa_asmbl_2460.p1, internal, 43044, 43166
-recovered pasa_asmbl_2460.p1, internal, 43575, 43804
-recovered pasa_asmbl_2460.p1, internal, 43977, 44160
-recovered pasa_asmbl_2460.p1, internal, 44280, 44432
-recovered pasa_asmbl_2460.p1, internal, 44942, 44964
Valid prediction for snap_scaffold_1-snap.2816-T1
Valid prediction for pasa_asmbl_2463.p1
Valid prediction for snap_scaffold_1-snap.2802-T1
Valid prediction for snap_scaffold_1-snap.2801-T1
Valid prediction for Augustus_model.g1562.t1
Valid prediction for snap_scaffold_1-snap.2819-T1
Valid prediction for Augustus_model.g1577.t1
Valid prediction for GlimmerHMM_glimmerT_2105-T1
Valid prediction for snap_scaffold_1-snap.2797-T1
Valid prediction for GlimmerHMM_glimmerT_2098-T1
Valid prediction for Augustus_model.g1563.t1
Valid prediction for snap_scaffold_1-snap.2795-T1
Valid prediction for GlimmerHMM_glimmerT_2114-T1
Valid prediction for snap_scaffold_1-snap.2817-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_1-snap.2787-T1
Valid prediction for snap_scaffold_1-snap.2815-T1
Couldn't classify 43091, 43222
Sorry, prediction pasa_asmbl_971.p1 fails validation.
(CAG)	 CG	43091-43222	GT	CGG
(GAT)	 AG	43335-43545	GT	GAG
(GAC)	 AG	46101-46249	GT	TGG
(ATG)	 AG	48324-48482	CC	AAC
-recovered pasa_asmbl_971.p1, terminal, 48324, 48482
-recovered pasa_asmbl_971.p1, internal, 43335, 43545
-recovered pasa_asmbl_971.p1, internal, 46101, 46249
Valid prediction for snap_scaffold_1-snap.2790-T1
Valid prediction for Augustus_model.g1560.t1
Valid prediction for GlimmerHMM_glimmerT_2118-T1
Valid prediction for snap_scaffold_1-snap.2788-T1
Valid prediction for snap_scaffold_1-snap.2820-T1
Valid prediction for GlimmerHMM_glimmerT_2116-T1
Valid prediction for pasa_asmbl_969.p1
Valid prediction for GlimmerHMM_glimmerT_2110-T1
Valid prediction for snap_scaffold_1-snap.2813-T1
Valid prediction for GlimmerHMM_glimmerT_2094-T1
Valid prediction for GlimmerHMM_glimmerT_2113-T1
Valid prediction for snap_scaffold_1-snap.2811-T1
Valid prediction for Augustus_model.g1572.t1
Valid prediction for GlimmerHMM_glimmerT_2096-T1
Valid prediction for snap_scaffold_1-snap.2821-T1
Valid prediction for Augustus_model.g1561.t1
Valid prediction for snap_scaffold_1-snap.2798-T1
Valid prediction for snap_scaffold_1-snap.2792-T1
Valid prediction for GlimmerHMM_glimmerT_2112-T1
Valid prediction for CodingQuarry_transcript_2951-T1
Valid prediction for snap_scaffold_1-snap.2794-T1
Valid prediction for GlimmerHMM_glimmerT_2115-T1
Valid prediction for CodingQuarry_transcript_2949-T1
Valid prediction for Augustus_model.g1576.t1
Valid prediction for snap_scaffold_1-snap.2789-T1
Valid prediction for HiQ_model.g1573.t1
Valid prediction for snap_scaffold_1-snap.2806-T1
Valid prediction for snap_scaffold_1-snap.2809-T1
Valid prediction for snap_scaffold_1-snap.2796-T1
Valid prediction for GlimmerHMM_glimmerT_2095-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 127596, rend_intergenic: 127593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19115, rend_intergenic: 15498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35970, rend_intergenic: 33849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37307, rend_intergenic: 37306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43942, rend_intergenic: 40502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45850, rend_intergenic: 43986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70783, rend_intergenic: 69493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71919, rend_intergenic: 70788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81646, rend_intergenic: 80511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96225, rend_intergenic: 89147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128884, rend_intergenic: 113571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131945, rend_intergenic: 129432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136011
-exon list size: 279


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.6    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.8    
7.1    
7.5    
7.8    
8.2    
8.5    
8.9    
9.3    
9.6    
10.0    
10.3    
10.7    
11.0    
11.4    
11.7    
12.1    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.7    
16.0    
16.4    
16.7    
17.1    
17.4    
17.8    
18.1    
18.5    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.4    
21.7    
22.1    
22.4    
22.8    
23.1    
23.5    
23.8    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.7    
38.1    
38.4    
38.8    
39.1    
39.5    
39.9    
40.2    
40.6    
40.9    
41.3    
41.6    
42.0    
42.3    
42.7    
43.1    
43.4    
43.8    
44.1    
44.5    
44.8    
45.2    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.7    
48.0    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
52.0    
52.3    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.8    
55.2    
55.5    
55.9    
56.2    
56.6    
56.9    
57.3    
57.7    
58.0    
58.4    
58.7    
59.1    
59.4    
59.8    
60.1    
60.5    
60.9    
61.2    
61.6    
61.9    
62.3    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.2    
76.5    
76.9    
77.2    
77.6    
77.9    
78.3    
78.6    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.5    
81.9    
82.2    
82.6    
82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.4    
90.7    
91.1    
91.5    
91.8    
92.2    
92.5    
92.9    
93.2    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.4    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 24 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 127596, rend_intergenic: 127593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19115, rend_intergenic: 15498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35970, rend_intergenic: 33849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37307, rend_intergenic: 37306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43942, rend_intergenic: 40502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45850, rend_intergenic: 43986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70783, rend_intergenic: 69493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71919, rend_intergenic: 70788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81646, rend_intergenic: 80511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96225, rend_intergenic: 89147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128884, rend_intergenic: 113571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131945, rend_intergenic: 129432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support