-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_7034444-7244496

-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 GlimmerHMM_glimmerT_9621-T1
Valid prediction for Augustus_model.g6229.t1
Valid prediction for snap_scaffold_4-snap.1523-T1
Valid prediction for Augustus_model.g6232.t1
Valid prediction for snap_scaffold_4-snap.1533-T1
Valid prediction for snap_scaffold_4-snap.1527-T1
Valid prediction for snap_scaffold_4-snap.1525-T1
Valid prediction for CodingQuarry_transcript_49036-T1
Valid prediction for pasa_asmbl_41452.p1
Valid prediction for CodingQuarry_transcript_49041-T1
Valid prediction for CodingQuarry_transcript_49042-T1
Valid prediction for snap_scaffold_4-snap.1515-T1
Valid prediction for pasa_asmbl_41460.p1
Valid prediction for snap_scaffold_4-snap.1502-T1
Valid prediction for Augustus_model.g6227.t1
Valid prediction for GlimmerHMM_glimmerT_9609-T1
Valid prediction for pasa_asmbl_41470.p1
Valid prediction for snap_scaffold_4-snap.1503-T1
Valid prediction for CodingQuarry_transcript_49045-T1
Valid prediction for snap_scaffold_4-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_9610-T1
Couldn't classify 33448, 33655
Sorry, prediction pasa_asmbl_41456.p1 fails validation.
(ATG)	 AG	31451-31880	GT	AGG
(GCC)	 AG	32951-33158	GT	AGG
(CCC)	 AG	33448-33655	GT	AGG
-recovered pasa_asmbl_41456.p1, initial, 31451, 31880
-recovered pasa_asmbl_41456.p1, internal, 31451, 31880
-recovered pasa_asmbl_41456.p1, internal, 32951, 33158
-recovered pasa_asmbl_41456.p1, internal, 33448, 33655
Valid prediction for snap_scaffold_4-snap.1511-T1
Valid prediction for snap_scaffold_4-snap.1507-T1
Valid prediction for snap_scaffold_4-snap.1513-T1
Valid prediction for CodingQuarry_transcript_49046-T1
Valid prediction for CodingQuarry_transcript_49037-T1
Valid prediction for CodingQuarry_transcript_49044-T1
Valid prediction for Augustus_model.g6228.t1
Valid prediction for snap_scaffold_4-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_9622-T1
Valid prediction for HiQ_model.g6231.t1
Valid prediction for GlimmerHMM_glimmerT_9613-T1
Valid prediction for GlimmerHMM_glimmerT_9626-T1
Valid prediction for GlimmerHMM_glimmerT_9619-T1
Valid prediction for Augustus_model.g6247.t1
Valid prediction for GlimmerHMM_glimmerT_9606-T1
Valid prediction for snap_scaffold_4-snap.1506-T1
Valid prediction for snap_scaffold_4-snap.1531-T1
Couldn't classify 27463, 27607
Sorry, prediction pasa_asmbl_41455.p1 fails validation.
(ACC)	 AG	27463-27607	GT	CGG
(GTG)	 AG	28345-28502	GT	AGG
(GTA)	 AG	28641-28821	GT	AGG
(CGG)	 AG	29025-29188	AC	GAA
-recovered pasa_asmbl_41455.p1, terminal, 29025, 29188
-recovered pasa_asmbl_41455.p1, internal, 27463, 27607
-recovered pasa_asmbl_41455.p1, internal, 28345, 28502
-recovered pasa_asmbl_41455.p1, internal, 28641, 28821
Valid prediction for GlimmerHMM_glimmerT_9607-T1
Valid prediction for Augustus_model.g6230.t1
Valid prediction for Augustus_model.g6233.t1
Valid prediction for GlimmerHMM_glimmerT_9604-T1
Valid prediction for CodingQuarry_transcript_49039-T1
Valid prediction for Augustus_model.g6237.t1
Valid prediction for snap_scaffold_4-snap.1498-T1
Valid prediction for snap_scaffold_4-snap.1519-T1
Valid prediction for Augustus_model.g6235.t1
Valid prediction for snap_scaffold_4-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_9617-T1
Valid prediction for GlimmerHMM_glimmerT_9612-T1
Valid prediction for snap_scaffold_4-snap.1514-T1
Valid prediction for GlimmerHMM_glimmerT_9611-T1
Valid prediction for Augustus_model.g6240.t1
Valid prediction for CodingQuarry_transcript_49040-T1
Valid prediction for GlimmerHMM_glimmerT_9620-T1
Valid prediction for GlimmerHMM_glimmerT_9615-T1
Valid prediction for snap_scaffold_4-snap.1500-T1
Valid prediction for snap_scaffold_4-snap.1508-T1
Valid prediction for snap_scaffold_4-snap.1495-T1
Valid prediction for CodingQuarry_transcript_49043-T1
Valid prediction for snap_scaffold_4-snap.1540-T1
Valid prediction for snap_scaffold_4-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_9624-T1
Valid prediction for pasa_asmbl_41457.p1

-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.g6245.t1
Valid prediction for GlimmerHMM_glimmerT_9629-T1
Valid prediction for Augustus_model.g6243.t1
Valid prediction for snap_scaffold_4-snap.1504-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1526-T1
Valid prediction for snap_scaffold_4-snap.1524-T1
Valid prediction for snap_scaffold_4-snap.1499-T1
Valid prediction for Augustus_model.g6234.t1
Valid prediction for snap_scaffold_4-snap.1538-T1
Valid prediction for snap_scaffold_4-snap.1512-T1
Couldn't classify 32133, 32303
Sorry, prediction pasa_asmbl_42702.p2 fails validation.
(ATC)	 GA	32133-32303	GT	AGG
(GAG)	 AG	33915-34042	GT	AGG
(CTG)	 AG	34419-34443	AA	GAA
-recovered pasa_asmbl_42702.p2, terminal, 34419, 34443
-recovered pasa_asmbl_42702.p2, internal, 33915, 34042
Valid prediction for snap_scaffold_4-snap.1534-T1
Valid prediction for snap_scaffold_4-snap.1528-T1
Valid prediction for snap_scaffold_4-snap.1510-T1
Valid prediction for snap_scaffold_4-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_9608-T1
Valid prediction for snap_scaffold_4-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_9616-T1
Valid prediction for snap_scaffold_4-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_9618-T1
Valid prediction for snap_scaffold_4-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_9625-T1
Valid prediction for snap_scaffold_4-snap.1516-T1
Valid prediction for Augustus_model.g6242.t1
Valid prediction for Augustus_model.g6226.t1
Valid prediction for snap_scaffold_4-snap.1522-T1
Valid prediction for GlimmerHMM_glimmerT_9630-T1
Valid prediction for snap_scaffold_4-snap.1537-T1
Valid prediction for snap_scaffold_4-snap.1532-T1
Valid prediction for snap_scaffold_4-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_9605-T1
Valid prediction for CodingQuarry_transcript_49047-T1
Valid prediction for snap_scaffold_4-snap.1530-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_49035-T1
Valid prediction for snap_scaffold_4-snap.1517-T1
Valid prediction for snap_scaffold_4-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_9628-T1
Valid prediction for GlimmerHMM_glimmerT_9603-T1
Valid prediction for Augustus_model.g6238.t1
Valid prediction for GlimmerHMM_glimmerT_9627-T1
Valid prediction for GlimmerHMM_glimmerT_9614-T1
Valid prediction for Augustus_model.g6244.t1
Valid prediction for snap_scaffold_4-snap.1541-T1
Valid prediction for snap_scaffold_4-snap.1509-T1
Valid prediction for snap_scaffold_4-snap.1501-T1
Valid prediction for Augustus_model.g6225.t1
Couldn't classify 38666, 38761
Couldn't classify 43843, 43862
Sorry, prediction pasa_asmbl_43589.p1 fails validation.
(ATC)	 GC	38666-38761	GT	AGG
(ATC)	 AG	41180-41236	GT	TGG
(ACT)	 AG	41550-41601	GT	AGG
(GTT)	 AG	41757-41851	GT	CCG
(GTG)	 AG	43281-43332	GT	CGG
(TGG)	 AG	43843-43862	TT	GCT
add_exon() Sorry, pasa_asmbl_43589.p1 41550-41601-terminal-3 is invalid.
-recovered pasa_asmbl_43589.p1, terminal, 41550, 41601
-recovered pasa_asmbl_43589.p1, internal, 41180, 41236
-recovered pasa_asmbl_43589.p1, internal, 41550, 41601
-recovered pasa_asmbl_43589.p1, internal, 41757, 41851
-recovered pasa_asmbl_43589.p1, internal, 43281, 43332
Valid prediction for Augustus_model.g6241.t1
Valid prediction for GlimmerHMM_glimmerT_9623-T1
Valid prediction for Augustus_model.g6246.t1
Valid prediction for Augustus_model.g6236.t1
Valid prediction for Augustus_model.g6239.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9910, rend_intergenic: 6927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18257, rend_intergenic: 15130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24688, rend_intergenic: 22173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29188, rend_intergenic: 25141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43402, rend_intergenic: 41392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90766, rend_intergenic: 79055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120692, rend_intergenic: 117425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129959, rend_intergenic: 122450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142852, rend_intergenic: 130359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146749, rend_intergenic: 144412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151507, rend_intergenic: 148526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169448, rend_intergenic: 165924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171905, rend_intergenic: 171224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174098, rend_intergenic: 172143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175101, rend_intergenic: 174393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207856, rend_intergenic: 202352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210053
-exon list size: 432


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9910, rend_intergenic: 6927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18257, rend_intergenic: 15130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24688, rend_intergenic: 22173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29188, rend_intergenic: 25141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43402, rend_intergenic: 41392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90766, rend_intergenic: 79055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120692, rend_intergenic: 117425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129959, rend_intergenic: 122450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142852, rend_intergenic: 130359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146749, rend_intergenic: 144412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151507, rend_intergenic: 148526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169448, rend_intergenic: 165924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171905, rend_intergenic: 171224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174098, rend_intergenic: 172143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175101, rend_intergenic: 174393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207856, rend_intergenic: 202352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support