-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_6751949-6955133

-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_59014-T1
Valid prediction for snap_scaffold_28-snap.1550-T1
Valid prediction for GlimmerHMM_glimmerT_59010-T1
Valid prediction for snap_scaffold_28-snap.1538-T1
Valid prediction for GlimmerHMM_glimmerT_59030-T1
Valid prediction for GlimmerHMM_glimmerT_59023-T1
Valid prediction for GlimmerHMM_glimmerT_59015-T1
Valid prediction for GlimmerHMM_glimmerT_59026-T1
Valid prediction for Augustus_model.g39118.t1
Valid prediction for snap_scaffold_28-snap.1545-T1
Valid prediction for snap_scaffold_28-snap.1533-T1
Valid prediction for snap_scaffold_28-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_59031-T1
Valid prediction for GlimmerHMM_glimmerT_59035-T1
Valid prediction for Augustus_model.g39120.t1
Valid prediction for snap_scaffold_28-snap.1520-T1
Valid prediction for Augustus_model.g39121.t1
Valid prediction for Augustus_model.g39115.t1
Valid prediction for GlimmerHMM_glimmerT_59006-T1
Valid prediction for snap_scaffold_28-snap.1558-T1
Valid prediction for snap_scaffold_28-snap.1551-T1
Valid prediction for snap_scaffold_28-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_59027-T1
Valid prediction for Augustus_model.g39110.t1
Valid prediction for snap_scaffold_28-snap.1556-T1
Valid prediction for snap_scaffold_28-snap.1557-T1
Couldn't classify 137430, 137450
Sorry, prediction pasa_asmbl_37632.p1 fails validation.
(ATG)	 TG	134884-134936	GT	TCG
(GTT)	 AG	135262-135376	GT	AGG
(GAT)	 AG	135765-135917	GT	GGG
(GTG)	 AG	137430-137450	GG	GGG
-recovered pasa_asmbl_37632.p1, initial, 134884, 134936
-recovered pasa_asmbl_37632.p1, internal, 135262, 135376
-recovered pasa_asmbl_37632.p1, internal, 135765, 135917
Valid prediction for GlimmerHMM_glimmerT_59008-T1
Valid prediction for snap_scaffold_28-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_59018-T1
Valid prediction for GlimmerHMM_glimmerT_59028-T1
Valid prediction for snap_scaffold_28-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_59012-T1
Valid prediction for snap_scaffold_28-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_59007-T1
Valid prediction for snap_scaffold_28-snap.1524-T1
Valid prediction for snap_scaffold_28-snap.1539-T1
Valid prediction for snap_scaffold_28-snap.1522-T1
Valid prediction for Augustus_model.g39111.t1
Valid prediction for snap_scaffold_28-snap.1549-T1
Valid prediction for snap_scaffold_28-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_59029-T1
Valid prediction for GlimmerHMM_glimmerT_59033-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_28-snap.1537-T1
Valid prediction for GlimmerHMM_glimmerT_59038-T1
Valid prediction for Augustus_model.g39114.t1
Valid prediction for snap_scaffold_28-snap.1529-T1
Valid prediction for snap_scaffold_28-snap.1553-T1
Valid prediction for GlimmerHMM_glimmerT_59022-T1
Couldn't classify 42996, 43165
Couldn't classify 43304, 43325
Sorry, prediction CodingQuarry_transcript_43696-T1 fails validation.
(ATG)	 AC	42996-43165	GG	GGG
(TCT)	 GG	43304-43325	AC	GAA
Valid prediction for snap_scaffold_28-snap.1536-T1
Valid prediction for snap_scaffold_28-snap.1530-T1
Valid prediction for snap_scaffold_28-snap.1525-T1
Valid prediction for snap_scaffold_28-snap.1523-T1
Valid prediction for snap_scaffold_28-snap.1543-T1
Valid prediction for Augustus_model.g39119.t1
Valid prediction for Augustus_model.g39117.t1
Valid prediction for GlimmerHMM_glimmerT_59011-T1
Valid prediction for snap_scaffold_28-snap.1547-T1
Valid prediction for GlimmerHMM_glimmerT_59009-T1
Valid prediction for HiQ_model.g39124.t1
Valid prediction for Augustus_model.g39113.t1
Couldn't classify 43181, 43228
Couldn't classify 43255, 43321
Sorry, prediction CodingQuarry_transcript_43695-T1 fails validation.
(ATG)	 AC	42996-43153	GT	GGG
(CTG)	 TA	43181-43228	AG	GGA
(TCC)	 GG	43255-43321	AT	AGA
-recovered CodingQuarry_transcript_43695-T1, initial, 42996, 43153
Valid prediction for snap_scaffold_28-snap.1532-T1
Valid prediction for snap_scaffold_28-snap.1546-T1
Valid prediction for snap_scaffold_28-snap.1519-T1
Valid prediction for GlimmerHMM_glimmerT_59019-T1
Valid prediction for Augustus_model.g39116.t1
Valid prediction for CodingQuarry_transcript_43698-T1
Valid prediction for Augustus_model.g39123.t1
Valid prediction for GlimmerHMM_glimmerT_59037-T1
Valid prediction for GlimmerHMM_glimmerT_59034-T1
Valid prediction for GlimmerHMM_glimmerT_59013-T1
Valid prediction for GlimmerHMM_glimmerT_59032-T1
Valid prediction for Augustus_model.g39126.t1
Valid prediction for GlimmerHMM_glimmerT_59021-T1
Valid prediction for GlimmerHMM_glimmerT_59036-T1
Valid prediction for snap_scaffold_28-snap.1554-T1
Valid prediction for CodingQuarry_transcript_43697-T1
Valid prediction for snap_scaffold_28-snap.1541-T1
Valid prediction for snap_scaffold_28-snap.1527-T1
Valid prediction for snap_scaffold_28-snap.1540-T1
Valid prediction for GlimmerHMM_glimmerT_59024-T1
Valid prediction for GlimmerHMM_glimmerT_59016-T1
Valid prediction for snap_scaffold_28-snap.1542-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1544-T1
Valid prediction for Augustus_model.g39112.t1
Valid prediction for snap_scaffold_28-snap.1552-T1
Valid prediction for snap_scaffold_28-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_59020-T1
Valid prediction for snap_scaffold_28-snap.1548-T1
Valid prediction for Augustus_model.g39125.t1
Valid prediction for GlimmerHMM_glimmerT_59025-T1
Valid prediction for Augustus_model.g39122.t1
Valid prediction for GlimmerHMM_glimmerT_59017-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11981, rend_intergenic: 5604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18665, rend_intergenic: 15002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22184, rend_intergenic: 20307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31312, rend_intergenic: 24444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32324, rend_intergenic: 31389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42611, rend_intergenic: 33497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45900, rend_intergenic: 44646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49727, rend_intergenic: 46471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63939, rend_intergenic: 49790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66908, rend_intergenic: 64608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82360, rend_intergenic: 67041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129507, rend_intergenic: 82538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142431, rend_intergenic: 130602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160595, rend_intergenic: 144473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167378, rend_intergenic: 160668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198063, rend_intergenic: 185206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203185
-exon list size: 390


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11981, rend_intergenic: 5604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18665, rend_intergenic: 15002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22184, rend_intergenic: 20307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31312, rend_intergenic: 24444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32324, rend_intergenic: 31389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42611, rend_intergenic: 33497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45900, rend_intergenic: 44646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49727, rend_intergenic: 46471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63939, rend_intergenic: 49790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66908, rend_intergenic: 64608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82360, rend_intergenic: 67041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129507, rend_intergenic: 82538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142431, rend_intergenic: 130602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160595, rend_intergenic: 144473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167378, rend_intergenic: 160668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198063, rend_intergenic: 185206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support