-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_10153915-10304956

-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 CodingQuarry_transcript_35792-T1
Valid prediction for CodingQuarry_transcript_35793-T1
Valid prediction for pasa_asmbl_31843.p1
Valid prediction for CodingQuarry_transcript_35790-T1
Valid prediction for snap_scaffold_23-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_51699-T1
Valid prediction for GlimmerHMM_glimmerT_51686-T1
Valid prediction for GlimmerHMM_glimmerT_51704-T1
Valid prediction for CodingQuarry_transcript_35791-T1
Valid prediction for pasa_asmbl_31836.p1
Valid prediction for GlimmerHMM_glimmerT_51707-T1
Valid prediction for GlimmerHMM_glimmerT_51700-T1
Valid prediction for HiQ_model.g34551.t1
Valid prediction for Augustus_model.g34556.t1
Valid prediction for GlimmerHMM_glimmerT_51692-T1
Valid prediction for GlimmerHMM_glimmerT_51697-T1
Valid prediction for snap_scaffold_23-snap.1968-T1
Valid prediction for snap_scaffold_23-snap.1949-T1
Valid prediction for snap_scaffold_23-snap.1962-T1
Valid prediction for Augustus_model.g34557.t1
Valid prediction for GlimmerHMM_glimmerT_51696-T1
Valid prediction for snap_scaffold_23-snap.1967-T1
Valid prediction for Augustus_model.g34554.t1
Valid prediction for pasa_asmbl_31845.p1
Valid prediction for snap_scaffold_23-snap.1973-T1
Valid prediction for snap_scaffold_23-snap.1955-T1
Valid prediction for pasa_asmbl_31839.p1
Valid prediction for Augustus_model.g34546.t1
Valid prediction for GlimmerHMM_glimmerT_51698-T1
Valid prediction for GlimmerHMM_glimmerT_51695-T1
Valid prediction for Augustus_model.g34553.t1
Valid prediction for HiQ_model.g34549.t1
Valid prediction for snap_scaffold_23-snap.1978-T1
Valid prediction for HiQ_model.g34545.t1
Valid prediction for snap_scaffold_23-snap.1972-T1
Valid prediction for GlimmerHMM_glimmerT_51688-T1
Valid prediction for snap_scaffold_23-snap.1975-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_35786-T1
Valid prediction for Augustus_model.g34558.t1
Valid prediction for GlimmerHMM_glimmerT_51689-T1
Valid prediction for snap_scaffold_23-snap.1951-T1
Valid prediction for snap_scaffold_23-snap.1964-T1
Valid prediction for GlimmerHMM_glimmerT_51703-T1
Couldn't classify 10171, 10224
Sorry, prediction pasa_asmbl_31834.p2 fails validation.
(ATG)	 CC	6269-6378	GT	ACG
(CGA)	 AG	6707-6757	GT	AGG
(GTA)	 AG	8445-8541	GT	AGG
(GAT)	 AG	8826-8961	GT	TGG
(GAA)	 AG	9219-9302	GT	AGG
(GGT)	 AG	9443-9531	GT	AGG
(GTG)	 AG	10171-10224	AG	TCA
-recovered pasa_asmbl_31834.p2, initial, 6269, 6378
-recovered pasa_asmbl_31834.p2, internal, 6707, 6757
-recovered pasa_asmbl_31834.p2, internal, 8445, 8541
-recovered pasa_asmbl_31834.p2, internal, 8826, 8961
-recovered pasa_asmbl_31834.p2, internal, 9219, 9302
-recovered pasa_asmbl_31834.p2, internal, 9443, 9531
Valid prediction for GlimmerHMM_glimmerT_51694-T1
Valid prediction for snap_scaffold_23-snap.1961-T1
Valid prediction for snap_scaffold_23-snap.1969-T1
Valid prediction for HiQ_model.g34552.t1
Valid prediction for GlimmerHMM_glimmerT_51705-T1
Valid prediction for GlimmerHMM_glimmerT_51702-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.g34544.t1
Valid prediction for snap_scaffold_23-snap.1974-T1
Valid prediction for snap_scaffold_23-snap.1970-T1
Valid prediction for Augustus_model.g34547.t1
Valid prediction for Augustus_model.g34555.t1
Valid prediction for GlimmerHMM_glimmerT_51693-T1
Valid prediction for GlimmerHMM_glimmerT_51706-T1
Valid prediction for snap_scaffold_23-snap.1976-T1
Valid prediction for snap_scaffold_23-snap.1971-T1
Valid prediction for snap_scaffold_23-snap.1957-T1
Valid prediction for snap_scaffold_23-snap.1952-T1
Couldn't classify 45714, 46577
Sorry, prediction pasa_asmbl_31143.p1 fails validation.
(GGT)	 CA	45714-46577	GA	GAG
Valid prediction for snap_scaffold_23-snap.1966-T1
Valid prediction for snap_scaffold_23-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_51685-T1
Valid prediction for GlimmerHMM_glimmerT_51690-T1
Valid prediction for GlimmerHMM_glimmerT_51701-T1
Valid prediction for snap_scaffold_23-snap.1963-T1
Valid prediction for snap_scaffold_23-snap.1977-T1
Valid prediction for Augustus_model.g34550.t1
Valid prediction for Augustus_model.g34559.t1
Valid prediction for GlimmerHMM_glimmerT_51708-T1
Valid prediction for snap_scaffold_23-snap.1948-T1
Valid prediction for snap_scaffold_23-snap.1954-T1
Valid prediction for snap_scaffold_23-snap.1959-T1
Couldn't classify 102597, 102628
Sorry, prediction pasa_asmbl_31139.p1 fails validation.
(TCC)	 GA	102597-102628	GT	AGG
(TAA)	 AG	102722-102800	GT	AGG
(GCA)	 AG	103145-103243	GT	AGG
(GCC)	 AG	105456-105617	GT	AGG
(GCC)	 AG	106305-106379	GT	AGG
(ATG)	 AG	106737-106811	GT	TGG
(ATG)	 AG	107482-107700	GT	AGG
(GTG)	 AG	109393-109518	GT	AGG
(GTG)	 AG	110033-110210	GT	AGG
(CTT)	 AG	110448-110596	GT	AGG
(GTG)	 AG	111667-111885	GC	AGG
-recovered pasa_asmbl_31139.p1, initial, 106737, 106811
-recovered pasa_asmbl_31139.p1, initial, 107482, 107700
-recovered pasa_asmbl_31139.p1, terminal, 111667, 111885
-recovered pasa_asmbl_31139.p1, internal, 102722, 102800
-recovered pasa_asmbl_31139.p1, internal, 103145, 103243
-recovered pasa_asmbl_31139.p1, internal, 105456, 105617
-recovered pasa_asmbl_31139.p1, internal, 106305, 106379
-recovered pasa_asmbl_31139.p1, internal, 106737, 106811
-recovered pasa_asmbl_31139.p1, internal, 107482, 107700
-recovered pasa_asmbl_31139.p1, internal, 109393, 109518
-recovered pasa_asmbl_31139.p1, internal, 110033, 110210
-recovered pasa_asmbl_31139.p1, internal, 110448, 110596
-recovered pasa_asmbl_31139.p1, internal, 111667, 111885
Couldn't classify 102722, 102887
Sorry, prediction pasa_asmbl_31135.p1 fails validation.
(ATG)	 GA	100710-100885	GT	AGG
(TAA)	 AG	102722-102887	GA	GGG
-recovered pasa_asmbl_31135.p1, initial, 100710, 100885
Valid prediction for snap_scaffold_23-snap.1953-T1
Valid prediction for GlimmerHMM_glimmerT_51691-T1
Valid prediction for HiQ_model.g34548.t1
Valid prediction for snap_scaffold_23-snap.1950-T1
Valid prediction for snap_scaffold_23-snap.1960-T1
Valid prediction for GlimmerHMM_glimmerT_51687-T1
Valid prediction for CodingQuarry_transcript_35788-T1
Valid prediction for snap_scaffold_23-snap.1965-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_35789-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11942, rend_intergenic: 6986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19817, rend_intergenic: 14983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46459, rend_intergenic: 40844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59718, rend_intergenic: 57343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70130, rend_intergenic: 67161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76872, rend_intergenic: 72912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87110, rend_intergenic: 78494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97321, rend_intergenic: 88129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124077, rend_intergenic: 111418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129021, rend_intergenic: 124156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136554, rend_intergenic: 131633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144025, rend_intergenic: 140750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151042
-exon list size: 315


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 11942, rend_intergenic: 6986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19817, rend_intergenic: 14983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46459, rend_intergenic: 40844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59718, rend_intergenic: 57343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70130, rend_intergenic: 67161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76872, rend_intergenic: 72912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87110, rend_intergenic: 78494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97321, rend_intergenic: 88129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124077, rend_intergenic: 111418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129021, rend_intergenic: 124156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136554, rend_intergenic: 131633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144025, rend_intergenic: 140750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support